The Sea of Japan was strongly stratified during the Last Glacial Maximum due to constant freshwater supply. We developed a multilayer box model to investigate paleo-oceanic dynamics that led to destratification triggered by the subduction of dense Oyashio water from the Tsugaru Strait. The Oyashio water subducted into the intermediate layer, which made the upper layer more saline through upwelling and vertical diffusion of saline seawater, thus weakening the stratification by salinity within the upper layer. This salinity also maintained the deep convection process triggered by sea ice formation during successive winters by increasing the surface salinity, and hence, density, of the upper layer. The bottom layer increased in thickness due to the persistent deep convection, thus gradually moving the subduction depth of the saline Oyashio water upward. This process accelerated the salinity increase in the upper layer, resulting in the rapid destratification and cessation of benthic hypoxia on a millennium timescale after the Last Glacial Maximum, even without considering sea level increase. Our model suggests the significance of the combination of Oyashio water subduction and deep convection in the paleo-oceanic dynamics of the Sea of Japan. It is concluded that both the subduction of saline Oyashio water from the Tsugaru Strait and deep convection are necessary to explain the destratification of the water column during deglaciation.