Chronic stroke patients are often unable to control their joint movements independently due to abnormal synergies. In our previous work, three robot-assisted therapy indices (two biomechanical indices and one electromyography assessment) were applied to quantify the abnormal synergies of upper limbs with the aid of a neuro-rehabilitation robot. In this study, these quantitative indices are employed to investigate the time course of abnormal synergies in the affected upper limbs of chronic stroke patients treated with the robot. Eight chronic stroke patients arc recruited to perform rectilinear tracking movements in four directions (back-forth. two oblique movements at 45 degrees, and right-left) during robot-assisted treatments for 4 months and 4 months of follow-up. The robot-assisted therapy indices (variation of forearm pronation/supination torque, and co-activation of elbow and shoulder muscles) reveal a significant decrease of abnormal synergies after 4 month s of robot-assisted treatment and a slight regression in the following 4 months. Significant recovery is found in motor outcomes evaluated using Brunnstrom stage and Fugl-Mcyer assessments. Both the robot-assisted therapy indices and clinical scales indicate modifications in abnormal synergies. The rectilinear tracking movements along the contra-proximal to ipsi-distal directions and the right-left directions are suitable for robot-assisted movement treatment for reducing abnormal synergies.