According to TMZ, who first reported the split, Ashlee filed the papers in Los Angeles Superior Court on Wednesday, citing "irreconcilable differences" as the reason for the split from her rocker beau.
The couple began dating in 2006 and wed in May 2008.
In her filing, Ashlee is seeking primary physical custody and joint legal custody of the couple's only child, their 2-year-old son, Bronx Mowgli Wentz.
Ashlee, 26, is also requesting the court grant her spousal and child support from Pete, 31.
In the filing, Ashlee has also requested her name be restored to Ashlee Nicole Simpson, and is seeking to terminate the court's ability to award spousal support to Pete.
Ashlee - a musician and actress - and Pete - who gained fame as a member of Fall Out Boy and has also worked as a successful music producer - tied the knot in a private ceremony held at the Simpson family home in Encino, Calif., back in 2008.
Ashlee's father, Joe Simpson, reportedly married the couple, while her big sister, Jessica, served as maid of honor.
In October 2009, Pete opened up to People magazine about the couple's plans for more kids.
"Everything is awesome about being a dad," he told the mag at the time. "Eventually we want to be able to have a soccer team."
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- Access Hollywood