Accurate rehabilitation assessments are essential for designing effective rehabilitation methods and helping patients recover better. It's well known that commonly used scale assessment methods for neurorehabilitation suffer from the issue of subjectivity, thus investigation of objective assessment methods is very necessary. Muscle synergy analysis can be uesd to assess limb motor functions from the perspective of neuromuscular control. In this paper, a method for evaluation of human lower limb motor functions based on muscle synergy analysis is presented. Muscle synergy modules are designed using surface electromyography (sEMG) signals of the subjects' lower limbs by non-negative matrix factorizations (NMF). By comparing the cosine similarities of these synergy modules, it can be seen that muscle synergies of healthy subjects and patients are significantly different, while they are similar among healthy subjects. Therefore, a reference synergy module (RSM) is designed by averaging the muscle synergy modules for healthy subjects, and the similarities can be calculated by comparing the synergy modules for healthy subjects or patients with the RSM. In the experiment carried out in this study, average similarities of the three synergy modules for healthy subjects are respectively 0.97166, 0.87368 and 0.84932, and on the other hand, the average similarities for the three synergy modules for patients are respectively 0.59979, 0.56426 and 0.69042. Therefore, the similarities for healthy subjects are much higher than those for SCI patients, which denotes that the similarity between an individual synergy module and the RSM can be used as an objective assessing index for evaluating patients' motor function.