Background: Ectopic thymoma, a subtype of thymomas, is a rare clinical entity. Understanding the pathogenesis and evolution of Ectopic thymoma may lead to greater insight into tumor initiation and maintenance and may guide therapeutic interventions. We report a case of a multiple thymoma in the lung and anterior mediastinum.Case presentation: we presented a case of 62-year-old man with type A ectopic pulmonary thymoma and thymoma in the anterior mediastinum, which were diagnosed postoperatively. Mediastinal lesion resection and thoracoscopic pulmonary wedge resection were performed. The tumors were completely resected, and the patient was disease-free and without recurrence. we performed whole-exome sequencing (WES), and found eight gene mutations that was co-mutated in both lesions. Consistent with a previous exome sequencing analysis of Thymoma and Thymic Carcinoma, HRAS was also observed in mediastinal lesion and lung lesion tissues. We also evaluated the intratumor heterogeneity of nonsilent mutations, and the mediastinal lesion tissue has higher degree of heterogeneity in detected variants, and the pulmonary tissue has a relatively low amount of variant heterogeneity. Conclusions: Ectopic thymoma is a highly rare clinical entity. Full recognition of its Molecular characteristics will help to better diagnose this disease.