Hecking, who took over in late 2012 and led Wolfsburg to second place and victory in the German Cup in 2015, has seen his team glean just six points this season despite making significant new signings, such as Germany striker Mario Gomez.
The 2009 German champions won only the first of their seven games and have lost three of their last four.
Hecking had trained with the team earlier on Monday.
"After the last few disappointing results we took the decision to give the team new impulses through a change of coaching staff," sports director Klaus Allofs said in a statement.
"On a personal level I feel sorry for this decision. In these intense almost four years we worked very successfully together."
Wolfsburg are in 14th place after losing 1-0 at home against RB Leipzig on Sunday.
Hecking said: "Obviously I am disappointed but that is part of this business, to expect such separations when there is no success. Unfortunately that was the case recently."
Under-23 coach Valerien Ismael will take over on an interim basis and prepare the team for their league game against Darmstadt 98 at the weekend.
(Reporting by Karolos Grohmann; Editing by Ian Chadband and Clare Fallon)
