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.
Maryland point guard Melo Trimble, considered a lock to leave the program before struggling in the second half last season, has withdrawn from the NBA draft and will return for his junior season.
Louisville's Chinanu Onuaku, who recently underwent a medical procedure to correct a heart rhythm issue detected during the combine, will keep his name in the NBA draft pool.
Andrew White III will return to the Nebraska men's basketball team next season after removing his name from the NBA draft.