Background and Aims: Although thymoma is inextricably linked to autoimmune disease, its best treatment method remains unclear. In this study, we sought to evaluate therapeutic effect of surgical resection of thymoma on non-myasthenia gravis autoimmune diseases. Materials and Methods: This was a retrospective study covering 32 patients with thymoma accompanied with non-myasthenia gravis autoimmune disease. The relationships between surgical treatment, thymoma pathological type, and prognosis of autoimmune diseases were analyzed from postoperative follow-up data. Results: In total, 32 patients in this study underwent surgical treatment. The mean age of the patients was 51.7 years. By the last follow-up, 2 patients had died, while the other 30 patients showed no sign of tumor recurrence and metastasis. According to the postoperative follow-up data, 22 patients (68.75%) showed improvement or even complete recovery of autoimmune disease symptoms, 9 patients (28.13%) showed no significant change, and only 1 patient’s (3.12%) postoperative symptom was aggravated. Female patients and patients aged 50 and older were more likely to combine with non-organ-specific autoimmune diseases (p = 0.036, p = 0.017). Conclusion: In conclusion, this study presents that surgical treatment achieves a satisfactory prognosis for thymoma combined with non-myasthenia gravis autoimmune disease.