Objective To evaluate the risk factors affecting the prognosis in patients with myasthenia gravis after thymeetomy. Methods Therapeutic effects were evaluated with Relative Counting Method in 136 cases with myasthenia gravis who receivingthymectomy. Six clinical factors including sex, age, preoperative course, et al. were converted into quantitative parameters and used for analysis. Cumulative logit model for ordinal response was employed to investigate the therapeutic effects of various factors. Results Sex, age and preoperative course exerted significant effects on postoperative prognosis in patients with myasthenia gravis, while clinical subtype, pathological changes and preoperative administration of cholinesterase inhibitors had no significant impact on therapeutic effects. Conclusion Some factors may lead to the remission and improvement in postoperative patients with myasthenia gravis, therefore, they should be included for the evaluation of prognosis. Early diagnosis and early thymeetomy may improve the therapeutic effects and shorten the duration of amelioration.