Myasthenia gravis (MG) is a neurological disease caused by autoantibodies targeting the neuromuscular junction. MG is frequently associated with thymoma, yet the cellular and molecular mechanisms in the thymoma are poorly understood. Here, using large-scale bulk RNAseq from the thymoma, we identified aberrant expression of neuronal molecules in MG thymoma. We also revealed that targets of autoantibodies present in the thymoma causing neuromuscular disorders notably enriched in the MG-type thymoma. Using single-cell RNA sequencing, we constructed the first comprehensive atlas of thymoma as well as that of the thymus with myasthenia gravis. Our single-cell analysis identified neuromuscular medullary thymic epithelial cells (nmTECs) as the source of the neuromuscular molecules. We also observed type 2 conventional dendritic cell (cDC2) migration, the B-cell maturation with ectopic germinal center formations, T follicular helper cells enhancement in MG thymoma. nmTECs actively interacted with T and B cells via a ligand-receptor pair CXCL12-CXCR4, and also with endothelial cells. Integrative analysis elucidated the genetic effect on regulatory T cells and B cells, and most impressively, the enrichment of nmTECs along with germinal center B cells and cDC2 in MG. Altogether, this study confers the comprehensive landscape of thymoma-associated MG centered on nmTECs.