The 53-year-old, who plays Ben Linus, said the long hours and months apart has put pressure on his relationship with actress Carrie Preston, whom he wed in 1998.
Preston lives in the couple's home in New York while Emerson spends half the year on the set of the ABC drama in Hawaii.
He told the National Enquirer: "My wife was a big fan, a real 'Lost-aholic'. She told me I'd be crazy not to do it.
"[But] it's been uniquely challenging for us. With me being that far away from our home in New York for half the year, it's a struggle to keep our marriage alive."
He added: "Because we are so many times zones away, my wife and I have to plan just to do a simple thing like talking on the phone."