A control system controls a hybrid vehicle having an engine for rotating a drive axle, an electric motor for assisting the engine in rotating the drive axle and converting kinetic energy of the drive axle into electric energy in a regenerative mode, and an electric energy storage unit connected through a drive control circuit to the electric motor, for storing electric energy. The control system has a regenerative quantity determining unit which includes first, second, and third first regenerative quantity establishing units. The first regenerative quantity establishing unit establishes a first regenerative quantity for the electric motor based on a vehicle speed of the hybrid vehicle when the supply of fuel to the engine is stopped upon deceleration of the hybrid vehicle. The second regenerative quantity establishing unit establishes a second regenerative quantity for the electric motor based on a remaining capacity of the electric energy storage unit. The third regenerative quantity establishing unit establishes a third regenerative quantity for the electric motor based on a temperature of the drive control circuit. A pumping loss controlling unit controls pumping losses of the engine based on the first, second, and third regenerative quantities.