The deals of both men were extended through the 2020 campaign. The Jets close this season against the New England Patriots on Sunday.
"We are very happy to have extended both Mike and Todd. During their time here, they have worked together to help the organization build a foundation on which to grow," Jets CEO Christopher Johnson said in a statement. "They are identifying, developing, and getting productivity out of our players. I believe we are headed in the right direction.
"This provides us continuity and stability as we continue to move this team towards sustained success. We still have a lot of work to do and I am excited to work closely with both of them as we move forward."
Bowles is 20-27 in his three seasons with the Jets. The team started 3-2 this season before collapsing with eight setbacks in the past 10 games.
Bowles said the team has made progress this season.
"Obviously, the future is trying to win a Super Bowl and trying to get to the playoffs," Bowles said. "We'll add some pieces. We made some strides this year. Not enough strides, not winning enough games, but going forward we'll make the proper adjustments and go from there."
Maccagnan is also finishing up his third season with the team. He has landed key players like defensive end Leonard Williams and safety Jamal Adams in the draft but the squad doesn't have a long-term answer at quarterback.
New York went 10-6 in 2015 in the first season of the Bowles/Maccagnan era. The club dropped to 5-11 in 2016.