Cruise's attorney, Bert Fields said to falsely claim the actor deserted his daughter is a "vicious lie."
"Tom is a caring father who dearly loves Suri. She's a vital part of his life and always will be," Fields said. "To say it in lurid headlines with a tearful picture of Suri is reprehensible."
The lawsuit was filed in a Los Angeles federal court.
An email message left for a spokeswoman for Bauer Publishing, which produces Life & Style, was not immediately returned.
Cruise and Suri's mother, Katie Holmes, were divorced earlier this year. They had been married for six years. The breakup has been tabloid fodder, and Suri often appears in entertainment magazines.
Cruise doesn't like to file lawsuits but felt it was appropriate because "sleaze peddlers" are trying to make money about the actor's relationship with his daughter, Fields said.
"These serial defamers are foreign-owned companies with their global headquarters in Hamburg," Fields said. "They take money from unsuspecting Americans by selling their malicious garbage. Having to pay a libel judgment may slow them down."
If Cruise prevails, Fields said his client would give the money to charity.