There are growing evidences that the warming marginal seas impact the torrential rainfall events in many parts of the world. The sea surface temperature (SST) in the East Asian marginal seas (EAMS) exhibits rapid rise during the last decades compared to the global mean, but its impact is still a matter of debate. Here we assess the impact of the recent warming trend of the EAMSs on the torrential rainfall event that caused devastating flooding and landslides in Kyushu Island located in the western part of Japan in July 2017, using a high-resolution cloud permitting model. The warming trend of EAMS with atmospheric warming since 1980s increases the simulated 12-hr precipitation to 6.8%, corresponding to approximately 10% increase per 1 K of SST rise, consistent with the previous data analysis study. Slight increase in heat and moisture supplies due to the warming EAMS has impacted a conditionally unstable condition of air masses flowing into an area of the precipitation, leading to more vigorous convective systems. Moisture budget analysis indicates that the changes in the amount of precipitation is not responsible for the availability of precipitable water but the intensification of the convective system. Since the change in precipitation amount exhibits high sensitivity to the SST trends, use of multiple SST datasets is desirable to provide a more reliable estimate and its uncertainty.