The 18-year-old, who had loan spells with Southend and Bury this season, has agreed a 12-month contract with the Latics having an option for a second year.
"When it comes to the risk and reward factor, Jonson is definitely worth it," manager Lee Johnson told the club's official website.
"He has all the attributes and potential to be a very good player.
"He is by no means the finished article and a lot of development work will be needed. And it is our job to do that because he could be anything he wants."
One of Clarke-Harris' four starts for Bury was against Latics last month at Gigg Lane where he caught the eye of Latics' manager Lee Johnson. He also made eight substitute appearances for the Shakers for whom he scored four goals.