The global distribution of zooplankton community structure is known to follow latitudinal temperature gradients: larger species in cooler, higher latitudinal regions. However, interspecific relationships between temperature and size in zooplankton communities have not been fully examined in terms of temporal variation. To re-examine the relationship on a temporal scale and the effects of climate control thereon, we investigated the variation in copepod size structure in the eastern and western subarctic North Pacific in 2000–2011. This report presents the first basin-scale comparison of zooplankton community changes in the North Pacific based on a fully standardized data set obtained from the Continuous Plankton Recorder (CPR) survey. We found an increase in copepod community size (CCS) after 2006–2007 in the both regions because of the increased dominance of large cold-water species. Sea surface temperature varied in an east–west dipole manner, showing the typical Pacific Decadal Oscillation pattern: cooling in the east and warming in the west after 2006–2007. The observed positive correlation between CCS and sea surface temperature in the western North Pacific was inconsistent with the conventional interspecific temperature–size relationship. We explained this discrepancy by the geographical shift of the upper boundary of the thermal niche, the 9°C isotherm, of large cold-water species. In the eastern North Pacific, the boundary stretched northeast, to cover a large part of the sampling area after 2006–2007. In contrast, in the western North Pacific, the isotherm location hardly changed and the sampling area remained within its thermal niche throughout the study period, despite the warming that occurred. Our study suggests that while a climate-induced basin-scale cool–warm cycle can alter copepod community size and might subsequently impact the functions of the marine ecosystem in the North Pacific, the interspecific temperature–size relationship is not invariant and that understanding region-specific processes linking climate and ecosystem is indispensable.