Young had five of Houston's six 3-pointers and Thomas also grabbed eight rebounds. Leon Gibson had 12 rebounds as Houston (9-3) took control early.
Chicago State (3-11) led briefly in the first three minutes, but Houston raced to a 40-25 halftime lead and was ahead by as many as 27 points in the second half.
Houston shot 45 percent in each half while Chicago State finished at 34 percent from the field.
Florida State's student government has passed a resolution discouraging Seminoles fans from wearing Native American headdresses at games.
The second annual Gavitt Tipoff Games, eight games between members of the Big East and Big Ten to be played Nov. 14-18, will feature Villanova at Purdue in the opener.
Michael Lewis is leaving his assistant coaching job at Butler to take the same position at Nebraska under Tim Miles.