Biomass pyramids in natural food webs provide insights into multitrophic ecosystem functioning. We measured the integrated trophic position (iTP), which reflects the average efficiency of biomass transfer through trophic pathways, of 14 mesozooplankton communities in the North Pacific. Compound-specific nitrogen isotope analysis of amino acids (CSIA-AA) for composite mesozooplankton biomass indicated that iTP of marine mesozooplankton communities was negatively correlated with species diversity. Offshore communities with lower diversity and higher iTP were dominated by large copepods such as Neocalanus, whereas onshore communities with higher diversity and lower iTP were characterized by several species belonging to Calanus, Paracaranidae, Eucalanidae, and Metridinidae. The observed iTP values (2.36 ± 0.32) indicate different topologies in biomass pyramids in different sites, where inverted pyramids are found in less diverse communities. The results suggest that the iTP values of marine mesozooplankton communities and their biomass pyramids are essentially controlled by biodiversity, body size, and species turnover.