The surf zone is an important habitat for larval organisms; in particular, a large amount of research has de- monstrated the utility of the surf zone as a nursery ground for various fish species. In last decade, concerns have arisen in China about this habitat, particularly around the Yangtze River estuary. Species composition, habitat selection, and biodiversity have been previously investigated. This study analyzed the characteristics of the larval fish assemblage in the surf zones of the Yangtze River estuary and Hangzhou Bay and determined the relative influences of various abiotic factors. Fish larvae were collected monthly using a small trawl net (1 m×4 m, 1-mm mesh size) at 12 stations during each spring tide from August 2009 to August 2010. Temperature, salinity, distance from the outermost site (km), landform, and substratum were simultaneously recorded at each sampling site. All collected specimens were fixed in 5% formalin, after which they were identified to the lowest possible taxonomic division and measured (length, mm). In total, 14907 individuals were caught by 462 hauls. The dominant species were (11.58%), Eleutheronema rhadinum (5.62%). Hierarchical clustering grouped the 13 months of sampling into 4 significant clusters(December–April, May, June–September, and October–November), showing clear species replacement among groups. The twelve stations were grouped into 2 groups: the Yangtze River estuary group (ST1–ST7) and the Hangzhou Bay group (ST8–ST12). SIMPER analysis indicated that the species contributing most to dissimilarity among groups were (>10%), indicating differentiation in habitat selection. Canonical correspondence analysis was performed on the same dissimilarity matrices. Salinity and temperature were significantly related to the distribution of larval and juvenile fishes, but did not significantly explain the total distribution, suggesting latent factors are influencing the assemblage. Generalized additive models were conducted for each primary species to reveal individual influencing environmental factors. The abundance of spp. were positively related to high temperature and sand substrata, while spp. were positively related only to high temperature. Two species in the genus P. japonica and were also positively related to sand substrata. In conclusion, this study revealed that temperature and salinity significantly affected spatiotemporal variation of the entire larval fish assemblages in the surf zones of the Yangtze River estuary and Hangzhou Bay, while substrata and landform had varying influence that differed among species. Habitats with sandy sediment and an open landform may be preferable to most larval fishes in the Yangtze River and Hangzhou Bay surf zones.