An unconfirmed report in the new issue of US magazine Us Weekly claims the low-key pair - who shun the spotlight - quietly agreed to separate earlier this year.
Reveal has reached out to reps for comment.
Megan and Brian have been together for eleven years and have two children together: sons Noah, two, and Bodhi, 18 months. Brian is also dad to 13-year-old son Kassius from a previous relationship.
After starting out as a child actress in films such as the Olsen Twins' Holiday In The Sun, it was action movie Transformers that turned Megan, now 29, into a worldwide star. She most recently starred in the Teenage Mutant Ninja Turtles reboot.
Meanwhile, Brian, 42, became famous for his role in Beverly Hills, 90210.
The couple met on the set of TV show Hope & Faith and became engaged in 2006. They called off their engagement three years later, before getting engaged again in 2010 and marrying a few days later at a small ceremony in Hawaii attended by just them and Brian's son Kassius.
Their first son Noah was born in 2012, followed by son Bodhi last year.