Geostrophic deep circulation in the Japan Sea is modeled using the primitive equation multilayer model developed by N.B. Shapiro and E.M. Mikhaylova (Marine Hydrophysical Istitute, RAS). The main simulated patterns are the cyclonic gyres along the sea margins and in the deep basins and the anticyclonic circulation above underwater rises, that generally corresponds with the schemes based on deep floats tracking. The deep circulation is more intense in the subarctic sector than in the subtropical sector and the most intense cyclonic gyre is simulated in the Japan Basin, with the current speed up to 7–8 cm/s at its eastern margin. Speed of the simulated currents compares well with that derived from Argo data. Weakening anticyclonic circulation in the southwestern part of the sea under forcing of cyclonic wind stress curl or decrease of volume transport in the Korea Strait causes increasing of the simulated deep currents in the entire sea and the cyclonic gyres in the whole water column in its subarctic sector. Therefore, the wind and thermal forcing indirectly affect the deep circulation through the water mass redistribution by the surface currents. The deep cyclonic gyre in the Japan Basin has strong seasonal variation, strengthening in winter and weakening in summer, in line with the buoys data. The gyre intensification is accompanied with its shrinkage and the current speed decreasing at its periphery, that explains the seasonal variation of the deep currents at the northern slope of the Japan Basin observed by deep mooring. This winter strengthening of the gyre, both in the deep and intermediate layers, increases the currents barotropy, whereas the gyre strengthening in the surface layer in summer, when it weakens below 100–150 m, increases the baroclinicity. Despite of relatively low spatial resolution, the model captures deep dynamic structures related to local bottom topographic features, such as anticyclonic eddies around underwater rises and seamounts and cyclonic eddies above topographic depressions in the subarctic sector. The reverse currents were simulated above Yamato Rise, Korea Plateau, and in the Ulleung Basin in condition of the weakened deep circulation adjusting in one or two months. The reverse currents are tracked by Argo buoys, too, they follow the changes of surface currents.