Abstract: To reveal spatial variation in trophic structure of nekton communities in the Zhejiang coastal Japanese anchovy (Engraulis japonicus) purse seine fishery and its drivers, we used carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) data from dorsal muscle of juvenile E. japonicus and bycatch species collected from May to June 2024, within the geographic coordinates of 27°50'–29°30'N and 121°37'–122°26'E. Trophic levels were estimated using Copepoda as the baseline organism. We integrated the Stable Isotope Bayesian Ellipses in R (SIBER) model with eight nutritional niche indicators and conducted cluster analysis to compare differences in the trophic structure of nekton communities associated with the Japanese anchovy fishery. The results indicate that δ¹³C is primarily influenced by species, with spatial effect being negligible. δ¹⁵N levels exhibit notable variations among sea areas and species. On average, δ¹⁵N values and trophic levels of various species in the southern Zhejiang sea area were significantly higher than those in the northern sea area. The trophic level of juvenile Japanese anchovy ranged from 2.23 to 3.68, increasing with the increase of body length, and is significantly higher in the south than in the north. Species such as Trachurus japonicus also showed significant differences in trophic level between the two seas. Cluster analysis categorized swimming animals into four trophic functional groups, forming a continuous trophic spectrum from plankton-feeding primary consumers to high-trophic-level carnivorous fishes. SIBER analysis indicates that the community in southern Zhejiang exhibited a broader ecological niche, greater nutritional diversity, and increased nutritional redundancy, whereas the overall ecological niche of the community in northern Zhejiang was comparatively narrower. This study employs stable isotopes of carbon and nitrogen to examine the nutritional composition and spatial variations of swimming animals in juvenile Japanese anchovy purse seine fishery along the coast of Zhejiang Province. The findings reveal that different water mass environments shape the trophic structure of nekton communities, thereby offering a scientific basis for regional fishery management.