The former Hendon boss joined the Beavers in June 2018 following the departure of Alan Dowson to Woking.
He helped keep Hampton stable in the National League South but this term has seen a season of struggle at the wrong end of the table.
The south west London clubs have won once in nine matches and Sunday’s 0-0 draw at home to Worthing means they are only outside the bottom four on goal difference.
McCann has had to contend with a crippling injury list this campaign but the club feel a change is needed to ensure survival.
Steve Bates, the academy manager, will take over on an interim basis.
A statement read: “It has been mutually agreed that Gary McCann will step down from his position as Manager.
“The club thanks Gary who has been an integral part of the club’s history.
“The club would also like to thank Gary and his management team for all their valuable contributions and considerable efforts over the past four years.
“The club will now start the recruitment process for Gary’s replacement.
“Academy Manager Steve Bates has assumed first team responsibilities on an interim basis.”
PHOTO: THOM LANG