Long‐term transition in the deep water of the Japan Sea was investigated to understand how oceans respond to climate change. A basin‐scale density decrease in the upper portion of the Japan Sea Proper Water (UJSPW) by 0.01 σθ was detected from the period 1964–1985 (Period I) to that of 2001–2019 (Period II) using Argo‐ and ship‐based data sets. The density decrease was mainly due to a temperature increase of 0.3°C. Based on the pycnostad density, the UJSPW was redefined as the water mass of 27.30–27.33 σθ, along with the core density of 27.30–27.31 σθ. The dissolved oxygen (DO) and thickness in the UJSPW showed a notable decrease between the periods, along with the isopycnal surfaces flattening. Warming down to 700 m and freshening in the upper 300 m were observed in the winter UJSPW formation area in the northwestern Japan Sea. An influence of the hemispheric‐scale regime shift occurred in 1988/1989 on the UJSPW warming was suggested, along with the long‐term trend in the winter air temperature. The freshening in the formation area was attributable to the increase in winter precipitation in the Amur River basin and the decrease in winter sea‐ice extents in the Okhotsk and northern Japan Seas. The intensified stratification in the UJSPW formation area brought a decrease in the amount of the UJSPW formation through the prevention of winter deep convection, which resulted in the thinner thickness and lower DO in the UJSPW in Period II, along with the temperature increase.