Introduction: Stroke is the second leading cause of death globally and a primary factor contributing to disability. Unilateral limb motor impairment caused by stroke is the most common scenario. The bilateral movement pattern plays a crucial role in assisting stroke survivors on the affected side to relearn lost skills. However, motion compensation often lead to decreased coordination between the limbs on both sides. Furthermore, muscle fatigue resulting from imbalanced force exertion on both sides of the limbs can also impact the rehabilitation outcomes.Method: In this study, an assessment method based on muscle synergy indicators was proposed to objectively quantify the impact of motion compensation issues on rehabilitation outcomes. Muscle synergy describes the body’s neuromuscular control mechanism, representing the coordinated activation of multiple muscles during movement. 8 post-stroke hemiplegia patients and 8 healthy subjects participated in this study. During hand-cycling tasks with different resistance levels, surface electromyography signals were synchronously collected from these participants before and after fatigue. Additionally, a simulated compensation experiment was set up for healthy participants to mimic various hemiparetic states observed in patients.Results and discussion: Synergy symmetry and synergy fusion were chosen as potential indicators for assessing motion compensation. The experimental results indicate significant differences in synergy symmetry and fusion levels between the healthy control group and the patient group (p ≤ 0.05), as well as between the healthy control group and the compensation group. Moreover, the analysis across different resistance levels showed no significant variations in the assessed indicators (p > 0.05), suggesting the utility of synergy symmetry and fusion indicators for the quantitative evaluation of compensation behaviors. Although muscle fatigue did not significantly alter the symmetry and fusion levels of bilateral synergies (p > 0.05), it did reduce the synergy repeatability across adjacent movement cycles, compromising movement stability and hindering patient recovery. Based on synergy symmetry and fusion indicators, the degree of bilateral motion compensation in patients can be quantitatively assessed, providing personalized recommendations for rehabilitation training and enhancing its effectiveness.