Anthropogenic climate change modifies the original geographic and seasonal variations of sea surface temperature (SST), which likely affects the temperature-dependent phenotypic patterns in aquatic organisms. The present study focuses on how growth pattern varies depending on the spatio-temporal variations of SST in an amphidromous fish ayu (Plecoglossus altivelis altivelis), distributed from the southwestern part of Hokkaido to Kagoshima. Using otolith increment- and trace element analyses, we compared latitudinal clines of growth rates (mm/day) and growth period (day) during the marine growth period between the Sea of Japan side (SJS) and Pacific Ocean side (POS) in 2001 (n = 231) and 2019 (n = 247). In the 2001 populations, growth rates showed negative latitudinal clines and growth period was shorter at lower latitudes in both SJS and POS. When compared at the same latitudes in SJS, fish collected in 2019 migrated to rivers at a younger age with faster marine growth than those in 2001. A similar trend was found across the middle-latitude to southernmost populations in POS, but was unclear in the northern populations of POS. Our findings are consistent with the patterns likely caused by the global warming-driven microgeographic/seasonal changes of coastal SST.