The actor will bow out from his role as John Barton early next year after portraying the character since 2009.
Thornton commented: "I have had a fantastic time playing John for the past three years, but it's the longest I have ever played one part and the time now feels right to move on.
"I have decided to leave on a high with a big exit storyline in 2012, which I'm really excited about. I will miss all my colleagues at Emmerdale and have many very fond memories of my time in the Dales."
Emmerdale's series producer Stuart Blackburn added: "James has created a truly memorable character in John and he will be greatly missed, but his decision to leave has enabled us to play a hugely gripping and dramatic storyline which will be a highlight in Emmerdale in the coming months."
John was recently left devastated when his wife Moira (Natalie J Robb) betrayed him by embarking on an affair with bad boy Cain Dingle (Jeff Hordley).
The farmer's fury over the situation will lead to him becoming a suspect when Cain is brutally attacked in a whodunit storyline which begins next week.
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