"I want to spend more time writing books and participating in the public debate in Denmark and abroad. The growing diversity in Europe has put freedom under pressure," Flemming Rose told the paper.
"It is a crucial debate that will determine the future of Europe," he added.
Rose was the culture editor of the right-wing Jyllands-Posten in 2005 when he commissioned 12 satirical cartoons blasphemous to Islam, triggering deadly protests in some Muslim countries.
Jyllands-Posten was the only major Danish daily that did not carry any illustrations from French satirical weekly Charlie Hebdo in the wake of the Paris attacks, citing security concerns.
"Jyllands-Posten has a lot to thank Flemming for. Through all (of his) 16 years he has made an outstanding contribution," wrote Jyllands-Posten's editor in chief, Jorn Mikkelsen.
Rose, Jyllands-Posten's foreign editor since 2010, has written two books about freedom of expression in a multicultural world.