The 22-year-old joined the Whites in September 2014 from Crewe Alexandra and made 30 appearances in all competitions, scoring twice.
Clayton, who will officially move to Bloomfield Road on July 1 following the expiry of his Bolton contract, told the official Blackpool website: "It's nice to come and get it over the line so quickly.
"I knew a few people here and I thought it was important for my development to come and work with people that I know. I want to contribute, I want to do well and I want to have an impact this season and hopefully push us up to have a good season."
Prior to joining Bolton, Clayton came through the youth system at hometown club Crewe, where he made 92 first-team appearances and scored 16 goals.