This study investigates stratification change in the southwestern East Sea (Japan Sea) using bi-monthly profile data of temperature and salinity measured by NFRDI (National Fisheries Research and Development Institute) for 36 years from 1971 to 2006. A linear trend analysis reveals that, in winter, the upper ocean (surface to about 100 m) has been warmed, while the subsurface (especially within the thermocline) has been cooled. This opposite trend intensifies stratification in the southwestern East Sea (Japan Sea) where the temperature mainly determines the density. Interestingly, the cooling trend is stronger than the warming trend. The similar changes are observed in summer, but with warming within shallower depth. The cooling trend in the subsurface is mainly attributed to the upward movement of the thermocline. This study suggests that the stratification increase in the southwestern East Sea (Japan Sea) is mainly associated with the cooling in the subsurface, rather than the upper ocean warming. 1971 to 2006. A linear trend analysis reveals that, in winter, the upper ocean (surface to about 100 m) has been warmed, while the subsurface (especially within the thermocline) has been cooled. This opposite trend intensifies stratification in the southwestern East Sea (Japan Sea) where the temperature mainly determines the density. Interestingly, the cooling trend is stronger than the warming trend. The similar changes are observed in summer, but with warming within shallower depth. The cooling trend in the subsurface is mainly attributed to the upward movement of the thermocline. This study suggests that the stratification increase in the southwestern East Sea (Japan Sea) is mainly associated with the cooling in the subsurface, rather than the upper ocean warming.