Paleoceanographic evidence commonly indicates that Last Glacial Maximum surface temperatures in the Japan Sea were comparable to modern conditions, in striking difference to colder neighboring regions. Here, based on a core from the central Japan Sea, our results show similar UK′37‐ and TEXL86‐derived temperatures between 24.7 and 16.3 ka BP, followed by an abrupt divergence at ~16.3 ka BP and a weakening of divergence after ~8.7 ka BP. We attribute this process to a highly stratified glacial upper ocean controlled by the East Asian Summer Monsoon, increasing thermal gradient between surface and subsurface layers during the deglaciation and the intrusion of Tsushima Warm Current since the mid‐Holocene, respectively. Therefore, we suggest that threshold‐like changes in upper‐ocean temperatures linked to sea level rise and monsoon dynamics, rather than just sea surface temperatures, play a critical role in shaping the thermal and ventilation history of this NW Pacific marginal sea.