The couple married September 2001 and has been legally separated since October 2009. Wonder cited irreconcilable differences in papers filed on Friday in Los Angeles Superior Court.
The 22-time Grammy winner used his legal name Stevland Morris for the papers, according to TMZ.
Wonder seeks joint custody of sons Kailand, 10, and seven-year-old Mandla. The 62-year-old also agreed of pay child and spousal support.
Wonder, Stevland Hardaway Judkins in real life, is a popular soul and R&B singer who is best known for his songs like "Superstition," "I Just Called To Say I Love You," and "Sir Duke." In 2009, he was named a United Nations Messenger of Peace.