The poleward expansion of coral habitats has been observed along the Japanese coast since the 1930s. Previous modeling studies have projected a poleward expansion using decadal-mean sea surface temperatures (SSTs) in the coldest months. However, this poleward expansion could be affected by the inter-annual variation of SST in the coldest months, which has not been considered before. In this study, the simulated pattern of poleward expansion was compared between cases where coral mortality was considered based on the inter-annual variation of SST and the decadal-mean SST in the coldest months. Modeled monthly mean SSTs for historical and future global warming simulations from the most recent climate projection model (MIROC4h) were used. The poleward expansion of corals simulated by considering mortality based on the inter-annual variation of SST in the coldest months better reproduced the observed poleward expansion speed compared to the simulations without such a consideration. Our results show the importance of considering coral mortality based on the inter-annual variation of seawater temperature to produce a more realistic poleward expansion of coral habitats.