The writer will finish his run with issue #6 of DC Comics' New 52 title, with Paul Jenkins joining the series in his place.
"I feel I should say something about stopping writing Stormwatch after #6, but there's not actually a lot to be said," Cornell wrote on his blog.
"It was my own choice, I wasn't sacked. It's not like there's chaos as a result: the first six issues set up a format for the title, and one of the reasons I chose that point to leave (quite a while back, this hasn't happened suddenly) was so a new writer can start with a solid foundation.
"Editor Pat McCallum has been a great custodian of longterm plans for the series, and he remains in place, so everything will go forward as it was meant to. If you're enjoying the series so far, you should feel able to keep buying it, because the underlying structure will remain."
Cornell will continue his work on DC's Demon Knights and said that he would "carry on liaising with the Stormwatch team about the links between the two titles".
He is also working on Vertigo's forthcoming Saucer Country for the publisher.
Stormwatch #5 will be released on January 4.