Western Kentucky's 466 yards of offense set a school record for total yards in a season with 5,565.
The win makes the Hilltoppers (6-5, 3-4 Conference USA) bowl eligible for the fourth-straight season.
Doughty threw TD passes to four receivers, including a 67-yarder to Willie McNeal for a 21-0 WKU lead. McNeal led all receivers with 105 yards on seven receptions.
Jared Dangerfield caught two TD passes, his second coming on a 16-yarder from Doughty, which gave the quarterback his 50th career touchdown pass.
The Roadrunners (3-8, 2-5) were held to 234 yards and avoided the shutout with a 47-yard touchdown pass from Dalton Strum to Kenny Thomas with 8:49 left to play.
