Understanding the role played by interspecies interactions, such as prey-predator relationships, in the structure of Earth’s ecosystem is a major challenge. The integrated trophic position (iTP), defined as a biomass-weighted average trophic position (TP) of a given food web, is a new proxy for food web structure that can be measured via stable isotope analysis. In this study, we investigated spatiotemporal variations in iTP by comparing compound-specific nitrogen isotopic compositions of amino acids in marine mesozooplankton communities collected from the cold Oyashio Current and the warm Kuroshio Current sites during 2012, 2017, and 2021. We found that (1) the iTP values in the Oyashio site with lower biodiversity are higher than those in the Kuroshio sites with higher biodiversity, suggesting that the trophic structure differs between the two sites; and (2) the iTP values were lowest in late spring at both sites, suggesting that phytoplankton bloom makes a bottom-up control on trophic transfer of energy. The results suggest that the iTP value of mesozooplankton communities is useful for capturing dynamic ecosystem structures in the ocean.