The 31-year-old midfielder - the Spireites's second new addition of the summer - made 36 appearances in the EFL Championship last season.
He's previously worked with Paul Cook at Portsmouth and admits he almost signed for his new boss at another side.
He told the club's Twitter: "It’s a great opportunity for me to come home. With what is going on at the club, it’s an exciting time.
"The gaffer is an experienced manager who has managed some big teams and been promoted a few times. I nearly signed for him at Wigan and I’m looking forward to working with him."
Naylor had played a pivotal role in the Latics winning the EFL League One title in 2021/22 and featured heavily last season.
The former Burton Albion and Mansfield Town man has signed a three-year deal at the SMH Group Stadium.
He follows Bailey Hobson through the door for the 2023/24 season as the Spireites look to bounce back from their Promotion Final defeat last season.
Don't forget the 2023/24 Vanarama National League season gets underway on Saturday 5 August - fixtures are out on Wednesday 5 July at 1pm.