Growth differentiation factor 11 (GDF11) has been reported to play a protective role in myocardial infarction. Mitochondrial DNA (mtDNA) damage is one of the pivotal factors in the initiation of myocardial cell damage. However, whether GDF11 can ameliorate mtDNA damage through its cardioprotective effect remains largely unknown. In this study, we obtained the GDF11-Fc fusion protein from mammalian cells and evaluated its cardioprotective effect in a mouse myocardial infarction model by TTC-Evans blue staining and morphological and enzymatic detection. Similar protective effects were observed in H9C2 cells and NRVMs. Mechanistically, we found that mtDNA damage was increased in I/R hearts. Exogenous administration of GDF11-Fc alleviated mtDNA damage and subsequent NLRP3 inflammasome activity, possibly through a reduction in ROS. In conclusion, GDF11 can ameliorate myocardial ischemia-reperfusion injury by inhibiting the inflammatory response induced by mtDNA damage.