Objective To study biological characteristics, prognosis and postoperative treatment in different clinical stages and pathologic types of thymoma. Methods Expressions of epithelial membrane antigen ( EMA) and Ki67 monoclonal antibody were detected by immunohistochemistry in thymoma resection specimens of 109 cases. The expression level of these antibody was respectively observed in different Masaoka stages and WHO pathological classification of thymoma, and statistical analysis was carried out. Results In different clinical stage and pathological type patients with thymoma, EMA negative or positive expression rate had no statistically significant difference, but from clinical stage Ⅱb and B₂ pathologic type, the expression intensity was gradually increased, and had the extremely significant difference ( P<0.01), differently compared with stage Ⅰ, stage Ⅱa, A type, AB type and B₁ type. Since stage Ⅱb and B₂ type, level Ⅲ and Ⅳ of Ki67 index increased significantly, and had very significant differonce ( P<0.01), compared with stage Ⅰ and Ⅱa and A, AB and type B₁. Conclusions The thymoma from Masaoka stage Ⅱb and the WHO classification type B₂ may have aggressive or malignant tendency, so postoperative adjuvant treatment measures should be taken.