The 65-year-old, who has been in charge at Gresty Road since June 1983, will become technical director of the club.
Academy manager Steve Holland will become first team coach - intially working alongside Gradi, before taking the reins completely.
"We are always planning our future, and have always had the plan that our next management would come from within the club," said Railywaymen chairman John Bowler.
"It was virtually impossible for us to bring someone in from the outside that would fit into our way of doing things.
"Steve is an integral part of what goes on at the club, he has had a big influence and now he has been given the chance to expand on that."