Helton led the Trojans to an 11-3 record in his second season as coach, including a victory in the Pac-12 Conference Championship game, earning USC its first Pac-12 title since 2008.
Helton, 45, overcame a turbulent start in 2017, losing three of his first four games, to lead USC to a 10-3 finish, including a win over Penn State in the Rose Bowl.
"Coaching at USC has been the most special opportunity of my life," Helton said in a statement. "And I am so pleased to continue the journey toward championships here."
He served as interim in 2013 following the departure of interim Ed Orgeron and led USC to a victory in the Las Vegas bowl.