Thymoma represents the most common anterior mediastinal compartment neoplasm, originating from the epithelial cell population in the thymus. Various histological types of thymoma feature different clinical characteristics. Furthermore, thymoma is frequently associated with autoimmune disorders, esp. myasthenia gravis (MG). However, the underlying molecular tumourigenesis of thymoma remains largely unknown. The goal of our current study is to demonstrate the underlying genetic abberations in thymoma, so as to understand the possible cause of MG in thymoma patients. By using CapitalBio mRNA microarray analysis, we analyzed 31 cases of thymoma including 5 cases of type AB thymoma, 6 B1-type cases, 12 B2-type cases, 5 B2B3-type cases and 3 type-B3 cases. 6 cases of thymoma were not associated with myasthenia gravis, while 25 cases were with myasthenia gravis. By comparisons between thymoma and the paratumoral tissues, differentially expressed genes were identified preliminarily. Among them, 292 genes increased more than 2-fold, 2 genes more than 5-fold. On the other hand, 596 genes were decreased more than 2-fold, 6 genes more than 20-fold. Interestingly, among these genes upregulated more than 2-fold, 6 driver genes (FANCI, NCAPD3, NCAPG, OXCT1, EPHA1 and MCM2) were formerly reported as driver oncogenes. This microarray results were further confirmed through real-time PCR. 8 most dysregulated genes were verified: E2F2, EPHA1, CCL25 and MCM2 were upregulated; and IL6, FABP4, CD36 and MYOC were downregulated. Supervised clustering heat map analysis of 2-fold upregulated and 2-fold downregulated genes revealed 6 distinct clusters. Strikingly, we found that cluster 1 was composed of two type-B2 thymoma; and cluster 6 was three type-B2/B3 thymoma. KEGG database analysis revealed possible genetic mechanisms of thymoma and functional process. We further compared gene expression pattern between thymoma with and without MG, and found 5 genes were upregulated more than 2-fold, more than 30 genes were downregulated more than 2-fold. KEGG analysis revealed 2 important signaling pathways with more than 2-fold upregulated genes (TGF-beta signaling pathway and HTLV-I signaling pathway) as differially functioning between MG positive and negative thymomas. Real-time PCR analysis confirmed that CCL25 was upregulated; and MYC, GADD45B, TNFRSF12 downregulated in thymoma with MG. Our study thus provided important genetic information on thymoma. It shed light on the molecular bases for analyzing the functional process of thymoma and finding potential biomarkers for pathological categorizing and treatment. Our work may provide important clues in understanding possible causes of MG in thymoma patients.