In 2023, the Kuroshio Extension (KE) exhibited an unusually large meander (LM) path, which caused a significant increase in sea surface temperatures, a marine heatwave (MHW), to the east of Japan. Although this MHW has the potential to influence heavy precipitation, it has not yet been examined. Here, we address this issue by examining an extreme precipitation event that occurred in Japan in September 2023 using high-resolution cloud-resolving numerical experiments. Results indicated that the MHW contributed to an increase in surface precipitation by ~ 300 mm, accounting for ~ 70% of the total precipitation. This precipitation intensification was attributed to the MHW-enhanced atmospheric instability and its influence on the formation and positioning of surface fronts. This research suggests that the KE-LM-induced MHW has elevated the risk of heavy precipitation in Japan, with significant societal implications. These findings could be applied to other regions such as the Northeastern United States.