The multi-decadal variation in ocean acidification indices in the Northwest Pacific was examined using a biogeochemical model with an operational ocean model product for the period 1993–2018. We found that ocean acidification varied regionally in the Northwest Pacific. The surface ocean (above 100 m depth) underwent acidification that progressed more quickly in the subtropical region and the Kuroshio extension than in the subarctic region due to vertical mixing of the dissolved inorganic carbon (DIC) supply exceeding DIC release by air–sea exchange. Below 100 m depth, acidification and alkalinization occurred in the subtropical and subarctic regions, respectively. We attribute these regional differences in acidification and alkalinization to spatially variable biological processes in the upper layer and physical redistribution of DIC, both horizontally and vertically.