Assistant manager Neil Cox will also leave the club, with first-team coach Simon Bassey to take over as interim boss.
Ardley was appointed Dons boss in 2012 and helped lead the club to great success but has struggled mightily this term.
A club statement read: "First team manager Neal Ardley is leaving the club by mutual agreement, with immediate effect.
"His assistant manager, Neil Cox, is leaving the club at the same time.
"First team coach Simon Bassey is taking over as interim manager while the search for a permanent successor to Neal gets underway.
"Ardley transformed the club from a playing and training point of view and also behind the scenes.
"His personal drive led to a major improvement in the training facilities both in terms of improved training pitches and the working conditions for the club staff.
"As a club, Wimbledon has always punched above its weight and Neal made sure we continued to do so for the following seasons culminating in winning a play-off final in 2015-16 where he led the team out at Wembley to fulfil a long term ambition.
"In the two seasons since that promotion Neal established us as a League One club despite the continued constraints on investment.
"Throughout his time with us he lived our values of openness and honesty.
"We thank him for the massive role he has played for us over the last six years and wish him well in his future career."
Ardley is a Wimbledon legend, having played for the club for a decade in the 1990s and early 2000s – racking up 245 league appearances.
But he has now been moved on, with chief executive Erik Samuelson adding: “Neal has been a credit to the club in everything he has done.
"He is a clear thinker, a superb man-manager and a fine coach. I’ve enjoyed working with him and am absolutely certain that he will achieve even greater success in his next roles.
"So, he leaves with my personal thanks and gratitude for what he has done in his time here at AFC Wimbledon."
AFC Wimbledon currently sit 23rd in League One with just three wins from 17 matches this season.
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