Strutton, 24, signed for the Dons last March and went on to make 17 appearances in total this year in what was his first full season, finding the net three times in the FA Cup.
Boss Neal Ardley told the club's official website: "Charlie had good impact in games, particularly at the end of last season, and he played a big part in us staying up.
"Charlie is still a bit raw and has had a few injuries in the last couple of years. However, if we can get a full season out of him or limit his time out injured then he can be a really good striker at this level."
Strutton himself added: "I am over the moon because this is what I wanted.
"I wanted to stay at Wimbledon, where I have enjoyed it a lot so far. I was not thinking about going anywhere else and I was just hoping that the club would offer me another contract. I am pleased that I have been offered a chance to stay."