Disclosed is a variable compression ratio control system configured to change a top dead center of a piston in an engine according to an operation state of the engine. The control system may include a motor provided as a power source, a control shaft coupled to the piston, wherein the control shaft changes the top dead center of the piston by a rotation of the control shaft, a driving shaft connected to the motor and to be rotated by the motor, an operation unit movable in a shaft direction of the driving shaft by a rotation of the driving shaft, and an operation link protruding from one portion of an exterior circumferential surface of the control shaft, wherein the operation unit is connected with the operation link so that the operation link rotates the control shaft while the operation unit moves in the shaft direction of the driving shaft.