The 29-year-old has agreed a two-and-a-half year extension which will see him stay at the club until 2015 after making 20 Premier League appearances so far this season
The 29-year-old has been a key member of Roberto Martinez's side this season, making 20 Premier League starts and scoring twice.
Martinez signed Maloney from Celtic in August 2011, and is pleased the Scotland international has extended his stay with the Latics.
"We're delighted that Shaun has committed his future to the club," the manager told the club's official website.
"From the first day he arrived his professionalism and determination to succeed has been outstanding and an example for the younger members of the group to follow."
Wigan go into Saturday's clash with Sunderland on Saturday lying in 17th place in the Premier League table, only out of the relegation zone on goal difference, and Martinez knows players like Maloney are key to ensuring top-flight survival.
"Shaun is one of the most technically gifted British players that you will find, but on top of his style and footballing flair his work-rate and purpose in his performances make him a key member of our future at Wigan Athletic," he added.
"I'm sure the fans are looking forward to watching him continue to enjoy his football at Latics for a long time."