"They broke up at least four months ago," a source tells Us. "They have gone their separate ways -- no bad blood."
Another source confirms there's no resentment between the two saying, "They just grew apart."
The couple started dating in summer 2012, and has kept a relatively low profile since.
Stan, 30, guest-starred on the popular ABC fantasy series as the Mad Hatter and last appeared on the show in October 2012 in Season 2. He is currently set to star in Captain America: The Winter Soldier as the super hero's friend-turned-opponent Bucky Barnes (aka The Winter Soldier), which hits theaters in April 2014.
Morrison, 34, currently stars in Once Upon a Time as Emma Swan, and was recently seen in the sci-fi sequel Star Trek Into Darkness in which she played Winona Kirk.
Prior to dating Morrison, Stan was linked to Glee star Dianna Agron, and from 2006 to 2007 Morrison was engaged to her House costar Jesse Spencer.