The 52-year-old veteran has signed a deal to drive the team's #00 Toyota in 25 races each year in 2012 and '13, replacing David Reutimann - who had been at the wheel of the car since 2007, winning the team's only two races thus far.
Martin's first race with MWR will be the 2012 Daytona 500, while Michael Waltrip will drive the car in the non-points Shootout in early February and the other restrictor-plate races of the season, as well as at Kentucky.
"[Sponsor] Aaron's and MWR have given me a chance to keep doing what I love with a competitive racecar and a perfect schedule for the next two years," said Martin.
"I have studied their programme, and, man, are they going in the right direction. I'm so impressed with what they are doing right now and I wanted to be a part of it. I want to help this organisation.
"This is like a rebirth. I just can't explain how excited I am to get to work."
In 2007 and '08 Martin drove partial schedules for Ginn Racing and Dale Earnhardt Inc, actually leading the standings after the first four races of '07 before skipping a race for the first time.
Martin said he was not considering any full-time drives looking ahead and revealed he held talks with Tony Stewart about driving a third car part-time for Stewart Haas Racing but said an agreement was "not even close". His deal with MWR came following three weeks of talks with Waltrip, with the contract only signed last Wednesday.
The addition of the NASCAR veteran to MWR is one of several announced over the past few months. Clint Bowyer will be joining the team full-time from next year, bringing Scott Miller with him from Richard Childress Racing to take over as executive vice president of competition.
The team will be fielding three cars next season for Martin Truex Jr, Bowyer and the #00 entry - which will have at least three different drivers, headed by Martin.
Michael Waltrip said his team still does not have a driver for those races where neither Martin nor Waltrip are not behind the wheel, while it still needs a sponsor for a handful of events as the Aaron's backing covers 30 rounds.
Starting the 2012 season aged 53, Martin could potentially become the oldest Cup race winner in the series' history.