Dinoflagellate cysts are commonly used to reconstruct past climatic, oceanographic and environmental conditions. Such applications are based on the relationship between modern dinoflagellate cysts and environmental parameters. To evaluate cyst diversity and driving factors of their distributions in sediments of the China Seas for paleoenvironmental reconstruction, dinoflagellate cysts were analyzed in 18 surface sediment samples from the Bohai Sea, the Yellow Sea (YS), the East China Sea and the South China Sea (SCS). A total of 59 dinoflagellate cyst taxa were identified with the greatest diversity reported in the SCS. The highest cyst concentrations were found in the YS, where Spiniferites ramosus, Spiniferites spp., and cysts of Pentapharsodinium spp. were predominant in the assemblages. The Yellow Sea Warm Current is likely creating the environment favoring the high numbers of Spiniferites ramosus in the YS. The highest Brigantedinium spp. abundances were observed near the Pearl River mouth and are positively correlated with sea-surface temperature (SST) in August. Spiniferites hyperacanthus, S. mirabilis, S. pacificus, and Lingulodinium spp. were most abundant in the SCS. In contrast, cysts of Protoperidinium spp. and Selenopemphix quanta were more common at the sites directly influenced by coastal upwelling rather than by river discharges. Redundancy Analysis results show that SST, sea-surface salinity (SSS) and nitrate concentration in water are statistically significant parameters influencing the cyst assemblages. We also examined the morphological characteristics of Spiniferites ramosus and recommend grouping S. bulloideus with S. ramosus in the northwest Pacific dataset for quantitatively reconstructing paleoceanographic conditions.