The actor, who plays troubled Aaron Livesy on the ITV1 show, will bow out from his role in spring 2012.
Miller commented: "It has been an incredibly difficult decision but after three years playing Aaron and much soul-searching, I am eager to explore other roles.
"I am so grateful to Emmerdale for the opportunity that I have been given and have loved every moment. I will miss everyone enormously but this might not be the last we see of Aaron."
Emmerdale's series producer Stuart Blackburn added: "We completely respect Danny's decision and are very grateful for the hard work and commitment he has brought to his role as Aaron. We wish him all the best for the future and in the meantime there is still plenty more drama to come from Aaron well into 2012."
Miller made his debut on Emmerdale in 2008. The character of Aaron had previously been portrayed by Danny Webb between 2003 and 2006.
Aaron has been involved in Emmerdale's most high-profile storylines in the past two years, which have included his struggle to accept his sexuality, a shock train crash stunt and a controversial assisted suicide plot centring around his boyfriend Jackson Walsh (Marc Silcock).
Miller has also won a string of 'Best Actor' and 'Best Dramatic Performance' awards for his portrayal of Aaron.
> Read more Emmerdale spoilers and news