The haptophytes, are essential components of the marine pico- and nano-plankton but little is known about their diversity and abundance due to the small size. In this study, the taxonomic composition, geographical distribution, and seasonal variation of the haptophytes in the Bohai Sea, the Yellow Sea, and the East China Sea were investigated using DNA metabarcoding in April and October of 2021. A total of 623 and 3756 haptophyte amplicon sequence variants (ASVs) were obtained in spring and autumn, respectively. All currently described or detected haptophyte orders were retrieved, including several deep-branching novel environmental lineages with relative high abundance. The predominant groups were Chrysochromulina, Clade HAP 2-3-4-5, Phaeocystis, and Prymnesium in spring, and Chrysochromulina, Phaeocystis, and Emiliania/Gephyrocapsa Compelx in autumn. The richness and diversity showed seasonal variation, with higher alpha diversity occurred in autumn than that of spring. Different haptophyte taxa exhibited unique spatial distribution patterns and water temperature was significantly correlated with the observed community dissimilarities and was the most influential driving factor in both seasons. Our results highlight the high hidden diversity and seasonal variations of haptophytes in the Chinese seas.