"It was time to go and leave Ole Miss," Hinson told the Daytona Beach (Florida) News-Journal on Wednesday. "I'm proud not to represent that flag anymore and to not be associated with anything representing the Confederacy."
Mississippi is on the verge of changing its state flag to erase the Confederate battle emblem following nationwide protests against racial injustice.
Ole Miss basketball coach Kermit Davis was among a contingent of 46 coaches and administrators from eight public universities who went to the state legislature Thursday to lobby for the emblem's removal.
Legislators are expected to start voting Sunday to remove the current flag from state law. A commission would design a new flag that cannot include the Confederate symbol and that must have the words "In God We Trust."
The SEC and NCAA both announced last week that NCAA postseason events would not be played in Mississippi until the state flag is changed. Conference USA, of which Southern Miss is a member, made a similar announcement Monday.
Hinson, who averaged 10.1 points and 4.6 rebounds per game last season, will join a Cyclones team that is also bringing in former DePaul guard Jalen Coleman-Lands as a graduate transfer but lost potential lottery pick Tyrese Haliburton to the NBA draft.
"I felt like it was the best option for me," Hinson told the newspaper of his decision to join the Cyclones. "There wasn't a real science that went into it. I looked into the schools and the play style, and I thought I fit best in Iowa State's system."
ESPN's Chris Low and The Associated Press contributed to this report.