The Chang-shan Archipelago is the largest island group in the northern waters of the Yellow Sea. It significantly contributes to local economic development due to its abundant aquatic products. In recent years, economically important shellfish (scallops, oysters, and clams) have exhibited growth retardation, thinning, and increased mortality, which has affected the sustainable and healthy development of fisheries. Marine microalgae are the dominant food source for filter-feeding shellfish; they differ in size, physiological functions, and sedimentation rates, which greatly influence the regional ecosystem food web.The microalgae size-fractions are closely related to the nutrient reserves and healthy growth of filter-feeding shellfish.High-throughput sequencing technology can reveal highly diverse eukaryotic lineages, while significantly reducing the errors associated with species identification, particularly microalgae. Importantly, the microalgae composition can be ascertained at multiple taxonomic levels, including at the species level. However, some questions still remain regarding their quantitative estimates. As the number of rDNA copies varies widely among different eukaryotes, it is difficult to determine the abundance of eukaryotic microalgae from rDNA CN-based inferences in environmental samples. However, related studies have demonstrated a significant positive correlation between rDNA sequence polymorphisms and rDNA copy numbersrate. When the size of the cell varies in a population, the rRNA/rDNA quantity reflects the biomass of that population. In this study, the proportion of rDNA copy numbers of eukaryotic microalgae was used to characterize their size distribution (the proportion of pico-, nano-, and microphytoplankton).In aquatic ecosystems, the factors controlling phytoplankton production and their seasonal successions are the main items of phytoplankton ecology. Several factors are linked to the growth and size-fraction structure of phytoplankton, such as the availability of light, temperature, nutrients, competition, and parasitism.Therefore, phytoplankton structure can be considered an integrator of environmental factors.In this study, we used the high-throughput sequencing method to assess the size-fraction structure of phytoplankton as well as the controlling environmental factors around the Changshan Islands. It showed that the proportion of pico-, nano-, and microphytoplankton was 42:47:39 in spring, 39:23:38 in summer, and 22:18:60 in autumn.Micromonas pusilla, Micromonas commoda, and Ostreococcus tauri were the dominant picophytoplankton; Karlodinium veneficum was the dominant nanophytoplankton; and Guinardia delicatula, Alexandrium hiranoi, and Gonyaulax polygramma were the dominant microphytoplankton around the Changshan Archipelago. Moreover, Karlodinium veneficum, Alexandrium hiranoi, and Gonyaulax polygramma were the dominant species in spring, summer, and autumn, respectively. The Mizuhopecten yessoensis selectivity to small and large microalgae was low, while the selectivity to medium microalgae was high, especially to Karlodinium veneficum, the dominant species in water. Environmental factors such as COD(chemical oxygen demand), DIN(dissolved inorganic nitrogen), DO(dissolved oxygen), Oil, Cd, As, and Hg were significantly related to the growth and size-fraction structure of phytoplankton. In the three seasons, Cd and COD were significantly related to the growth of picophytoplankton biomass; DO, DIN, and Oil were significantly related to the growth of picophytoplankton biomass; and COD, As, and Hg were significantly related to the growth of picophytoplankton biomass.