Brohm's Hilltoppers had a school-record 702 total yards against the defending MAC champions.
Western Kentucky raced to a 21-0 lead on Leon Allen's 2-yard run, and Doughty's 55-yard touchdown pass to Taywan Taylor, and 34-yarder to Atwane Grant.
Taylor finished with 12 catches for 185 yards and Jared Dangerfield had 10 catches for 92 yards and two touchdowns.
Bowling Green scored in the third quarter on Andre Givens' 3-yard run and Matt Johnson's 41-yard pass to Ronnie Moore. Johnson completed 25 of 36 passes for 314 yards.
Doughty countered with two more scoring strikes, finding Willie McNeal for 20 yards and Dangerfield from 5 yards out.
