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The following are noted differences between the City of Bones novel and the movie adaptation, The Mortal Instruments: City of Bones.

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Book Movie
Clary Fray was 15 years old and just turned 16 after Jocelyn went missing. Clary Fray was instead 17, turning 18.[1]
Simon Lewis's eyes are brown. Simon Lewis's eyes are green.
Isabelle Lightwood led the Eidolon demon into a storage room at the Pandemonium Club. Jace, Alec, and Isabelle kill it in the middle of the nightclub.
The Frays' apartment was trashed in search of the Mortal Cup. The apartment was in a worse condition because of the confrontation between Jocelyn, Samuel Blackwell and Emil Pangborn, and their search for the Cup. At the end of the movie, Clary returned to fix the damage with a rune.
Clary killed the demon in her apartment by shoving a Sensor down it's throat. Jace killed the demon, though Clary did weaken it when it disintegrated in an explosion in the kitchen.
The Ravener demon that waited for Clary in the apartment resembled "a cross between an alligator and centipede". The demon left in the apartment that attacked Clary was in the form of a dog and became octopus-like, but its tendril's somewhat resemble the long body described in the book.
Jace, Clary and Simon searched Luke's bookstore and hid when Luke arrived with Emil Pangborn and Samuel Blackwell until they all left. When Clary and Jace entered Luke's bookstore, leaving Simon outside, Luke was already inside and was being tortured by Pangborn and Blackwell. Clary asked Jace to save him and a fight broke out.
Vampires appear normal enough, aside from the occasional vampire trait such as their pale skin, that they can pass as ordinary mundanes. At Magnus's party, the vampires look normal apart from their pointed teeth and feral-looking eyes. In Hotel Dumort, the vampires resemble rotting zombies, albeit a bit more alive.
Simon was turned into a rat after he stubbornly drunk a magical blue cocktail at Magnus Bane's party and was accidentally taken by a vampire. Simon was drugged and intentionally kidnapped by vampires; they used him as bait to lure Clary and the other Shadowhunters into Hotel Dumort. He wasn't turned into a rat, but in a deleted scene, Simon did state that he "felt like a rat" while he was being held hostage.
Only Clary and Jace rescued Simon from Hotel Dumort. Alec and Isabelle joined the rescue.
Raphael Santiago helped Jace and Clary sneak into the Hotel Dumort. Jace, Clary, Isabelle and Alec entered the Hotel Dumort through the front door.
Luke sent members of his pack to follow Clary. Clary then threw a knife at one of the werewolves, Alaric; he later returned the knife to her and complimented her aim. Luke had been following Clary and was part of the raiding group and the fight at the hotel. It had also been Luke that Clary threw a knife at, and he would also later return it to her and commend her for it.
Simon did not become a vampire until City of Ashes. Simon already showed signs of becoming a vampire in the film: his eyesight had gotten better and he has two bite marks on his neck.
There was no mention of famous figures being Shadowhunters. Johann Sebastian Bach was a Shadowhunter, whose music can expose demons.
There is a Portal in Madame Dorothea's flat. There is no mention of a Portal in her flat.
There is no permanent Portal in the New York Institute. There is a Portal in the Institute. Going through the Portal creates small tremors that is felt through the Institute.
Portals require no skill to use. Shadowhunters train for long periods of time in the use of Portals, particularly to focus where the Portal would take them, else risk being stuck in limbo and losing one's sanity.
Clary asked Simon to borrow Eric's van and to drive them to Madame Dorothea's. Clary, Jace, Isabelle and Alec traveled to Madame Dorothea's on their own without Simon, though they run into Eric on their way. 
Jace, Isabelle and Alec find out that Madame Dorothea was (possessed by) a demon when she opened the Portal in her room. Jace was immediately suspicious of Dorothea and played a Bach piece on the piano to determine if she was one; when the demon in Dorothea was brought to the surface, Isabelle and Alec also realized it when their demon-detecting particles responded to her transformation.
Shadowhunters use Sensors to sense demons. Shadowhunters use a chunk of a metallic substance to sense demons.
Simon helped kill the Greater Demon Abbadon that possessed Dorothea by using Alec's bow and arrow to destroy the skylight in the hallway. Simon tackled Madame Dorothea through the front door of the apartment building after Clary told him she had the Cup.
Luke's pack resides in an abandoned police station with a Chinese restaurant front. They appear to be located in a car workshop called "Ed's Garage".
Clary Fray doesn't find out about her ability to make runes until City of Ashes. Clary learned relatively early that she can create runes.
The Fearless rune is not created until City of Ashes. There are some discrepancies with the movie's runes. The Fearless rune, for example, can be seen on the gear of the Shadowhunters. Additionally, the rune Clary "creates" to freeze the demons in one scene can also be seen upside-down on Valentine's chest and is even an existing rune ("Vision") in canon. Several other runes were used differently in the movie; in fact, the purposes of the different runes never seemed truly significant in the film.
Demons never entered the New York Institute. Demons were summoned into the Institute by Valentine.
Readers were led to believe that Jace and Clary were siblings. In a conversation with Valentine, Hodge revealed the former's intent to lie to Jace and Clary about them being related, making the viewers immediately aware.
Jace recognized Valentine as his 'father' and did not fight him. Jace's memories were apparently blocked, much like Clary's, and had to be "reminded" that Valentine raised him and remained doubtful and in denial even afterwards.
Valentine's hair is white-blond. Valentine's hair is brown.
Clary followed Hodge Starkweather to confront him for giving Jace and the Mortal Cup to Valentine, after which Valentine removed Hodge's curse (an actual one that kept him in the Institute). He tried to kill Clary, but Luke saved her and Hodge disappeared. Hodge left while Valentine was summoning demons, after the latter insisted that he was not cursed and it has all been in his head. Hodge then helped Isabelle and Simon shut down the pentagram.
The fight at the end of the book, which involved Jace, Valentine, Luke, Pangborn, Blackwell, Valentine's Forsaken warriors, and Luke's new pack followers, took place at Renwick's. The fight took place in the Institute with the groups separated.
Valentine successfully stole the Cup. Clary managed to trick Valentine with a replica of the Cup and was still in possession of the real one at the end of the film.
Valentine willingly entered the Portal to Idris in his escape. Clary had to push Valentine into the Portal.
Alec recovered and forgave Clary for their previous argument. Alec was last seen being treated, and his condition apparently improving, by Magnus Bane.
Jocelyn was rescued at Renwick's. Clary did not know if there was a chance that she could still wake up. Jocelyn was brought to the Institute by Valentine. Clary saw Jocelyn's finger quiver under her touch.
In their escape from the Hotel Dumort, Jace took Clary for a ride on a vampire's bike before sunrise above the river of New York. Jace came by Clary and Jocelyn's apartment with a normal bike and took her back to the Institute on it.
Valentine did not know that Jocelyn was pregnant with their second child until years after. In a deleted flashback scene, Jocelyn's belly had already grown quite big while she was still with Valentine and their son.
Luke was a Shadowhunter and Valentine's parabatai, closest friend, and second-in-command in the Circle before the latter betrayed him. There was little indication of their past in the film, or even of Luke's past, aside from a deleted scene showing Valentine leading Luke into an ambush that Turned him into a werewolf.
Jace and Alec being parabatai plays a big part in their relationship. There is no mention of parabatais.
There were several other changes made in the film. If you know of any that we missed, feel free to add them here. If in doubt, place it on the talk page.

See also

References

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