The Qiangji Jianli Decoction (QJJLD) is an effective Chinese medicine formula for treating Myasthenia gravis (MG) in the clinic. QJJLD has been proven to regulate mitochondrial fusion and fission of skeletal muscle in myasthenia gravis. In this study, we investigated whether QJJLD plays a therapeutic role in regulating mitochondrial biogenesis in MG and explored the underlying mechanism. Rats were experimentally induced to establish autoimmune myasthenia gravis (EAMG) by subcutaneous immunization with R97–116 peptides. The treatment groups were administered three different dosages of QJJLD respectively. After the intervention of QJJLD, the pathological changes of gastrocnemius muscle in MG rats were significantly improved; SOD, GSH-Px, Na⁺-K⁺ ATPase and Ca²⁺-Mg²⁺ ATPase activities were increased; and MDA content was decreased in the gastrocnemius muscle. Moreover, AMPK, p38MAPK, PGC-1α, NRF-1, Tfam and COX IV mRNA and protein expression levels were also reversed by QJJLD. These results implied that QJJLD may provide a potential therapeutic strategy through promoting mitochondrial biogenesis to alleviate MG via activating the AMPK/PGC-1α signaling pathway.