Mesozooplankton biomass plays a key parameter in the recruitment processes of fish and biogeochemical processes. Four decadal observations in the coastal Sea of Japan, the marginal sea of the North Pacific, indicate that wet weight-based mesozooplankton biomass is controlled by both environment-induced bottom-up and predatory-induced top-down processes. Interannual variations in mesozooplankton biomass using a generalized linear model approach showed a decrease in biomass during the 1980s, followed by a rapid increase in the early 1990s, and a gradual decrease in the 2010s. These interannual variations were the mirror image of the small pelagic planktivorous fish biomass. The difference in zooplankton biomass from the previous year was negatively correlated with the difference in small pelagic planktivorous fish biomass, which was supported by a Granger causality analysis. Therefore, the results of this study indicate that top-down control is one of the main causes of long-term variations of zooplankton biomass in the ocean.