Earnhardt will work with Steve Letarte, who has been Gordon's crew chief since he replaced Robbie Loomis late in the 2005 season. Gordon will be paired with Alan Gustafson, who has been Martin's crew chief
Lance McGrew will move from Earnhardt to Martin.
The only combination left untouched was Jimmie Johnson and Chad Knaus, who on Sunday won their fifth straight championship.
In addition, Earnhardt's team will move into the facility that builds cars for Johnson. Gordon's cars will share a facility with Martin's, marking the first time since Johnson's team went full-time in 2002 that it was not housed in Gordon's shop.
"This will improve us as an organization, across the board," team owner Rick Hendrick said in a statement. "We had a championship season, but we weren't where we wanted and needed to be with all four teams. We've made the right adjustments, and I'm excited to go racing with this lineup."
While Johnson won six races and the title, Gordon, Earnhardt and Martin went winless and only Gordon made the Chase, finishing ninth. Martin finished 13th and Earnhardt 21st.
The move is as close as Hendrick could get to pairing Earnhardt with Knaus, who will work hand in hand with Letarte on turning around NASCAR's most popular driver.
"It's pretty obvious we aren't very good and we need to do some things to get better,'' Earnhardt said last weekend at Homestead-Miami Speedway. "It's obvious that's where we are. I don't think it needs to be overanalyzed or anything like that.
"The last couple of years have been hard. We've been bad. We ain't run good. I ain't run good. It's been real hard to deal with. ... I still feel some confidence in what I can do. I guess I'm just glad that's still there, you know?''
No further comment was available, but Hendrick will discuss the shakeup more on Wednesday.
David Newton covers NASCAR for ESPN.com. He can be reached at firstname.lastname@example.org.