The invention provides a position control apparatus of a flexible bilateral driving device, and the apparatus comprises a measure sensor, a position control unit and an execution unit, and the method comprises the following steps: the practical position of the measure sensor is measured, through transformation and compensation of the position control unit, the corrected position is transferred back to the device by the execution unit. The invention is capable of raising the synchronization capability of a system, raising the anti-interference performance; reducing or eliminating the servo error caused by the interference; realizing the precision positioning of a multi freedom system, minimizing stabilization time when accelerating or decelerating in a period for increasing the production capacity; greatly improving the non-linear damping adjustment, reducing the heat dissipation of a flexible body in a movement process, enhancing the anti-fatigue capability of the flexible body for prolonging the life for further. In addition, the invention provides a flexible bilateral driving device by using the position control apparatus which is capable of realizing the vibration damping of the workpiece bench and accurate position compensation.