"In a spirit of mutual respect, Racing Club de Lens and Dino Toppmoller announce, by mutual agreement, the end of their collaboration," Lens said in a statement.
The club said it had held extensive discussions with Toppmoller about the squad and the organisation of his coaching staff before informing him that it wanted to restructure the set-up.
"As Dino Toppmoeller could not agree to these structural changes, the Club, acting responsibly, has decided to bring his role to an end, as well as that of his two assistants," the French side added.
Toppmoller, 45, was appointed in June, following the departure of Pierre Sage, who joined Premier League side Crystal Palace after guiding Lens to a historic French Cup win and a second-place finish in Ligue 1.
The German manager, who was under contract until 2028, started his stint with a stunning 1-0 win against Paris Saint-Germain last month to win the Trophee des Champions.
In Ligue 1, Lens won only one of their first four matches, while they opened their Champions League campaign with a dramatic 3-2 victory at Slavia Prague.
They sit 10th in the Ligue 1 table before visiting Monaco on Friday with Yannick Cahuzac, who was Toppmoller's assistant, in the dugout.