Lynskey submitted legal forms to an LA court last week claiming that she and Simpson separated due to "irreconcilable differences", reports TMZ.
Neither Simpson nor Lynskey is seeking spousal support once the divorce is finalised.
The couple apparently ended their relationship in April, five years after they originally tied the knot.
Simpson apparently met Lynskey on the set of the Stephen King miniseries Rose Red in 2001.
Lynskey is best known for playing Charlie Harper's stalker-turned-lover Rose in Two and a Half Men, but has also had roles in the films Up in the Air and The Perks of Being a Wallflower.