Young, 68, filed a petition for dissolution of marriage on July 29, according to the report.
The couple were married in 1978 but famously met four years earlier when she was working as a waitress in northern California.
"She used to work in a diner, Never saw a woman look finer," Young sang on Unknown Legend, from 1992's Harvest Moon. "I used to order just to watch her float across the floor."
Pegi Young sang backup on her husband's albums and, beginning in 2007, has released three albums of her own.
The couple have two adult children — a daughter, and a son who has cerebral palsy. That inspired them to co-found The Bridge School in 1986 to help educate children born with severe physical disabilities.
Bridge School benefit concerts have taken place every year since, with another planned for Oct. 25-26 in Mountain View, Calif.
Young, per usual, has been busy with a number of projects this year. Earlier this year he released a cover song project, A Letter Home, recorded at Jack White's studio.
He's also been heavily involved in developing Pono, a high-quality audio music player, and has said he is combing the vaults for another archival release of previously unheard material.
The singer-songwriter was briefly married in the late 1960s, and lived with actress Carrie Snodgress in the early 1970s. Young and the late Snodgress had one son, who also has cerebral palsy, but a milder form than his younger brother.
A hearing on the divorce filing is scheduled for Dec. 12, according to the San Mateo, Calif., court website.