"Katharine is no longer seeing Michael -- at least for now," a source told the celebrity magazine.
Morris' wife, actress Mary McCormack, reportedly threw the director out of their home last month after he told her photos of him kissing McPhee were about to be published.
McPhee was separated from Nick Cokas, her husband of four years, at the time of the scandal.
"Katharine still has no plans to move forward with divorce at the moment, though they are not living together," the insider told People.com. "This is an incredibly hard time for Katharine."
McPhee and Morris met on the set of the now-canceled TV show "Smash."