Order of The Shadowhunter Chronicles by Cassandra Clare

The Shadowhunter Chronicles written by Cassandra Clare consists of four series, each of which has a different protagonist.

[ I ] The Mortal Instruments 

The Mortal Instruments is a series of six YA fantasy novels, whose protagonist is a teenage girl called Clary Fray. She stumbles across a group of Nephelim, who are Shadowhunters, while they are doing their usual job of hunting demons. Except she, as a mundane, isn't supposed to be able to see them. She is taken to the Shadowhunters' (Jace, Alec and Isabelle) home where she learns more about her own heritage and family history.

She meets various kinds of creatures as she continues to discover the Shadowhunter universe - warlocks, werewolves, vampires, demons and angels - and battles a lot of enemies alongside the others. 

The books of this series in reading order are - 

1. City of Bones 
2. City of Ashes 
3. City of Glass 
4. City of Fallen Angels 
5. City of Lost Souls 
6. City of Heavenly Fire 

[ II ] The Infernal Devices

This book deals with Tessa Gray, who moves to London and gets entangled in the lives of the Nephilim living there. This book is written in a time before the Mortal Instruments took place, and has few characters, but a gripping storyline.

At the Shadowhunter house, Tessa meets Will Herondale and Jem Carstairs, as well other Shadowhunters who help her adapt to her new life. Tessa has peculiar powers, as is a being like none of them have ever seen before. When enemies threaten their house, Tessa stands with the others to defend it and uncovers various secrets from her past.

The books of this series in reading order are - 

     1. Clockwork Angel  

     2. Clockwork Prince

     3. Clockwork Princess

[ III ] The Dark Artifices

The series follows Emma Carstairs and her journey as a Shadowhunter living in the Los Angeles Institute. She lives there with her best friend and parabatai, Julian Blackthorn and his family. Their parabatai bond makes them connected in a special way, and very powerful. However, there is one drawback - you are forbidden from falling in love with your parabatai. 

The Dark Artifices is a trilogy about their struggle against their enemies and how both of them deal with their forbidden love and its consequences. The series is written from the point-of-view of the different characters in the story.

The books of this series in reading order are -     

1. Lady Midnight 
2. Lord of Shadows
3. Queen of Air and Darkness

[ IV ] The Last Hours

This is the story of James and Lucie Herondale, in the Edwardian Era of London. They are accompanied by their parabatai, Matthew Fairchild and Cordelia Carstairs. Children of many of the characters from The Infernal Devices also star in this series, as well as the characters themselves, now older. The story moves back and forth between London, Paris, Cornwall and Idris (the home country of Shadowhunters).

Many of the misleading factors of the family tree as shown in the previous books are cleared up in this series. Some important objects and characters from the previous series also make an appearance here. 

The books of this series in reading order are -  

    1. Chain of Gold

    2. Chain of Iron

    3. Chain of Thorns

There are also other series and individual books written by the author, which tell us the life story of some of the side characters or give us more information about the Shadowhunter world.

The Eldest Curses -

1. The Red Scrolls of Magic
2. The Lost Book of the White

Books not a part of any series -

1. The Bane Chronicles
2. The Shadowhunter’s Codex
3. Tales from the Shadowhunter Academy
4. Ghosts of the Shadow Market