This study, based on samples taken in seven cruises from February 2003 to November 2004, linked larval fish assemblages with mesoscale oceanographic features dominated by the monsoon‐driven current system in the Taiwan Strait. A total of 7753 specimens of larval fish were identified from our samples, belonging to 467 taxa in 112 families and 230 genera. Engraulidae, Myctophidae, Scombridae, Carangidae, and Gobiidae were the five most abundant families. Three larval fish assemblages were distinguished by association respectively with the China Coastal Current, Kuroshio Branch Current, and South China Sea Surface Current, and accordingly designated as the cold‐period northern Taiwan Strait (CNTS), southern Taiwan Strait (STS), and warm‐period northern Taiwan Strait (WNTS) assemblages. The composition of larval fish differed significantly between assemblages, with the CNTS being the most dissimilar assemblage, probably due to the presence of neritic/oceanic taxa in the STS and WNTS and primarily neritic‐associated taxa in the CNTS. The alternate intrusions of currents in the Taiwan Strait driven by seasonal monsoons play a pivotal role in the dispersal and community structure of larval fish. In addition, winter front turbulence and local topographic upwelling contributed to the increase in biological production; consequently resulting in high chlorophyll a concentrations and zooplankton biomass to provide abundant food for the survival of larval fish. The high correlation between the environmental variables and the larval fish assemblages offers the possibility to use the assemblages as indicators of the surface circulation in the Taiwan Strait and thereby improve our understanding of the ecosystems.