"Joe was an integral part of our Big East championship in 2008, but we differ philosophically over where we want to go defensively in the future," Bearcats coach Brian Kelly said in a statement.
Cincinnati finished 31st in the nation in total defense (321.9 yards a game) and led the Big East in sacks during its run to the FedEx Orange Bowl. The Bearcats led the nation in turnovers and interceptions under Tresey in 2007.
Tresey joined Kelly at Central Michigan in 2006. He is the second assistant to leave Kelly's staff this offseason. Assistant head coach/defensive line coach Keith Gilmore went to Illinois earlier this month.
Brian Bennett covers the Big East for ESPN.com.