In this study, the interannual variations of ichthyoplankton assemblages in the Taiwan Strait (TS) during the winters of 2007–2013 were determined. The cold China Coastal Current (CCC) and Mixed China Coastal Water (MCCW) intruded into the TS and impinged with the warm Kuroshio Branch Current (KBC) with annual variations. Consequently, the ichthyoplankton community in the TS was mainly structured into two assemblages characterized by differing environmental conditions. The composition of the warm KBC assemblage was relatively stable and was characterized by Diaphus B and Bregmaceros spp. By contrast, the cold MCCW assemblage demonstrated considerable variations over the years, with demersal Gobiidae and Scorpaenidae families considered the most representative. In addition, Benthosema pterotum and Trichiurus spp. were common in both KBC and MCCW assemblages. The distribution of the KBC assemblage demonstrated sharp boundaries in the frontal zones, whereas changes in the assemblage structure between the frontal zones were gradual for the MCCW assemblage, particularly when demersal taxa were dominant. Sea surface temperature and salinity were most strongly associated with variability in the assemblage structure during the study period. Thus, this paper provides a better understanding of long-term larval fish dynamics during winter in the TS.