A family insider tells the magazine that Garner, 42, is about four months along and the pregnancy "came as a complete shock" to the couple -- though a rep for the actress is claiming it's not true.
"Ben has been going above and beyond lately: He's checking up on Jen all the time and surprising her with flowers," the source said, adding that the pregnancy has been helping their marriage.
"Jen thinks this baby could be the key to making her marriage strong again."
In April Affleck, 41, was caught counting cards in Las Vegas and an internal email from the Games Protection Manager at the Wynn and Encore casinos, Rob Olivetti, warned recipients that Affleck had been spotted counting cards.
A few days later, on April 28, he was banned from play at the Hard Rock Hotel & Casino over similar issues, and a local security firm issued an all-points bulletin announcing the news, including a picture of Affleck at the tables grabbed from a security camera.
Married in 2005, Garner and Affleck already have three children together: Violet Ann, 8, Seraphina Rose, 5, and Samuel Garner, 2.