The Kuroshio–Oyashio transitional zone (KOTZ), constituting the complex water–mass structure surrounding the oceanfront system, is one of the most important fisheries grounds in the western North Pacific. It serves as spawning and nursery sites among several commercially important fish species that consume appendicularians, particularly during the larval stages. In the present study, we investigated the species composition, abundance and biomass of appendicularian assemblages at 20 stations in the KOTZ in the summer of 2018. Appendicularian communities, including 24 species belonging to 7 genera—the highest record for the western North Pacific—were divided into three groups, corresponding to the anticyclonic eddy, a trough between the eddy and the Kuroshio Extension, and the rest of the study area. Statistically, the temperature within the surface layer and strength of water turbulence appear to strongly affect the quantitative and qualitative characteristics of the appendicularian community structure in the KOTZ. This relationship could be attributed to the effect of temperature on the population size and species coexistence, potentially offering an advantage for appendicularians in the future warming ocean scenario and the role of water turbulence in the predatory impact exerted by carnivores on appendicularians.