Us Weekly cites multiple sources confirming the pregnancy, which has been rumoured since May.
The Transformers star was also spotted with what it described as "an unmistakable baby bump" in Los Angeles on Thursday, June 7.
The couple, who first met on the set of the former ABC sitcom Hope & Faith, tied the knot in an intimate ceremony in Hawaii in June 2010.
Green is already a dad to a 9-year-old son named Kassius, whose mother is Vanessa Marcil of soap opera General Hospital fame.
Fox previously appeared in Friends with Kids and The Dictator. She is set to appear in the Judd Apatow-directed movie This Is 40.
> Megan Fox cuts off Steve Jones interview after baby question - video
Watch a trailer for The Dictator below: