To study the factors affecting the long-term prognosis of patients with myasthenia gravis (MG) after thymectomy. 170 MG patients who had undergone thymectomies were studied retrospectively. Among them, 124 patients received long-term follow-up for more than 40 months postoperatively. The COX regression analysis model was used to analyze the factors that may influence the long-term prognosis. These factors included thymus pathology, patient gender, age, duration of disease at the time of surgery, preoperative Osserman classification and medication. The research showed that thymus pathology was the single independent factor that affected the postoperative long-term prognosis. The long-term survival rates differed significantly with thymus pathological types: hyperplasia > benign thymoma > atrophy > malignant thymoma (P < 0.05). The different pathological types of the thymus were the important factor affecting long-term survival in MG patients after thymectomy.