The Chippewas (2-0) took control with a dominating second quarter, scoring 24 points and shutting down the Kansas offense with a pair of interceptions. They had picked off Rhode Island six times last week in a season-opening three-overtime victory.
Morris, a senior transfer from Michigan, lit up the KU secondary in the second period with touchdown passes to Mark Chapman, Lane Hessbrook and Corey Willis. Willis' TD reception capped a 90-yard drive in the final 66 seconds to give CMU a 24-6 lead at halftime.
Morris completed 28 of 37 passes.
The Jayhawks (1-1) looked to make a game of it in the third quarter with two quick touchdowns -- from receiver Ryan Schadler and running back Dom Williams -- but the Chippewas of the Mid-American Conference countered with a pair of scores and won going away behind the strong left arm of Morris.
Chapman caught eight passes for 168 yards and three touchdowns, including a 75-yarder in the fourth quarter that put the game away. Willis finished with eight catches for 140 yards and one score.
Kansas quarterback Peyton Bender, who threw for 364 yards and four touchdowns in last week's win over Southeast Missouri, struggled against the Chippewas. Bender threw for 323 yards, but completed just 32 of 62 passes and finished with two interceptions and no touchdowns. He was sacked twice.