Active movements are important in the rehabilitation training for patients with neurological motor disorders, while weight of upper limb impedes movements due to muscles weakness. The objective of this study is to develop a position-varying gravity compensation strategy for a cable-based rehabilitation robot. The control strategy can estimate real-time gravity torque according to position feedback. Then, the performance of this control strategy was compared with the other two kinds of gravity compensation strategies (i.e., without compensation and with fixed compensation) during movements tracking. Seven healthy subjects were invited to conduct tracking tasks along four different directions (i.e., upward, forward, leftward, and rightward). The performance of movements with different compensation strategies was compared in terms of root mean square error (RMSE) between target and actual moving trajectories, normalized jerk score (NJS), mean velocity ratio (MVR) of main motion direction, and the activation of six muscles. The results showed that there were significant effects in control strategies in all four directions with the RMSE and NJS values in the following order: without compensation > fixed compensation > position-varying compensation and MVR values in the following order: without compensation < fixed compensation < position-varying compensation (p < 0.05). Comparing with movements without compensation in all four directions, the activation of muscles during movements with position-varying compensation showed significant reductions, except the activations of triceps and in forward and leftward movements, the activations of upper trapezius and middle parts of deltoid in upward movements and the activations of posterior parts of deltoid in all four directions (p < 0.05). Therefore, with position-varying gravity compensation, the upper limb cable-based rehabilitation robotic system might assist subjects to perform movements with higher quality and improve the participation of robot-aided rehabilitation training. Further studies are needed to explore the effectiveness and clinic application across pathologies.