An electro-hydraulic load simulator (EHLS) is a typical case of torque systems with strong external disturbances from hydraulic motion systems. A new velocity synchronizing compensation strategy is proposed in this paper to eliminate motion disturbances, based on theoretical and experimental analysis of a structure invariance method and traditional velocity synchronizing compensation controller (TVSM). This strategy only uses the servo-valve's control signal of motion system and torque feedback of torque system, which could avoid the requirement on the velocity and acceleration signal in the structure invariance method, and effectively achieve a more accurate velocity synchronizing compensation in large loading conditions than a TVSM. In order to facilitate the implementation of this strategy in engineering cases, the selection rules for compensation parameters are proposed. It does not rely on any accurate information of structure parameters. This paper presents the comparison data of an EHLS with various typical operating conditions using three controllers, i.e., closed loop proportional integral derivative (PID) controller, TVSM, and the proposed improved velocity synchronizing controller. Experiments are conducted to confirm that the new strategy performs well against motion disturbances. It is more effective to improve the tracking accuracy and is a more appropriate choice for engineering applications.