We investigated temporal and spatial variations in the zooplankton community structure in the Oyashio and Transition region of the subarctic western North Pacific from 1960 to 1999 using principal component analysis (PCA) and zooplankton samples from the historical Odate Collection. In particular, we examined the influence of Kuroshio and Oyashio decadal dynamics on geographical variations in the zooplankton community. The first principal component (PC1) closely represented the interannual variation in cold-water, large copepod species, while the second PC (PC2) represented the variation in warm-water, small copepod species. Using Rodionov's regime-shift method, we detected a significant increase in the PC score after 1976 and 1981 for PC1 and PC2, respectively. After the shift years, (1) warm-water species increased in the Transition zone, (2) the distribution center of the cold-water species shifted southward, and (3) copepod abundance and species diversity increased in the Transition zone as a result of (1) and (2). The timing of these shifts in the zooplankton community roughly coincided with the North Pacific climatic regime shift in 1976/1977. From the mid-1970s to the early 1980s, the southern boundary of the Oyashio shifted southward and increased geostrophic transport was observed in the Kuroshio, indicating spin up of the Kuroshio–Oyashio system. Change in atmospheric circulation during the 1976/1977 regime shift is thought to have caused the spin up of these currents, which subsequently affected the regional zooplankton community through advective processes.