The pair, who share two-year-old daughter Briar Rose, has been "on the outs" for months and are living in separate cities, reported Us Weekly.
"She's full-time back in LA. He's in Toronto. They've been on the outs for a couple of months," a source said, adding that Bilson and Christensen, both 36, "are completely, officially done."
The pair has been infamously quiet about their relationship for years.
The couple first met on the set of their 2008 film "Jumper" and began dating that year. The got engaged later in December, but quietly called off their engagement in August 2010 only to reconcile three months later.
Bilson and Christensen were last seen together in June, when she visited him on set of his movie "Little Italy" in Toronto.