Based on the phytoplankton net samples from the Yellow Sea collected between 1985 and 2015, the interdecadal variations in the community structure were studied and the composition dissimilarities were analyzed. A total of 1125 samples were checked to establish the phytoplankton community structure, including 220 samples from the Northern Yellow Sea and 905 samples from the Southern Yellow Sea. Phytoplankton samples were preserved in 5% formalin water solution after each towing and were kept in dark until analysis. In the laboratory, sub-samples were analyzed for the identification of the species, which were counted using an optical microscope (Leica Biomed). Phytoplankton diversities were represented by species richness (Margalef index), species diversity (Shannon-Weaver index), and species evenness (Pielou index). The dominance of each taxon was calculated using the Dufrene-Legendre index and SIMPER analysis was performed in Past 3.18 software. A total of 81 genera and 202 species were recorded over the past 30 years, with diatoms and dinoflagellates being the major groups. There were 58 genera and 142 taxa of diatoms, 20 genera and 57 taxa of dinoflagellates, 2 genera and 2 species of silicoflagellates, and one species of . The species number of diatoms accounted for 62.4%, 69.1%, 74.4%, and 62.6% of the total in the 1980s, 1990s, 2000s, and 2010s, respectively. However, this proportion was only 47.5% during the summer seasons; in contrast to the dinoflagellate proportion, which was 52.3%. In 2005-2015, the dominant taxa were Protoperidinium in the Northern Yellow Sea, while in the Southern Yellow Sea, they were . As for the species ecotypes, there were no obvious variations in the eurythermal species, which were 67.4% and 71.8% during 1985-2000 and 2005-2015 century, respectively. However, during 2005-2015, there was an average increase in warm water species of 10.3%. The interdecadal average abundance of total phytoplankton was 76.2×10⁴ ind/m³, of which 80.3% was diatoms, which declined to 67.5% during 1985-2000. During 2005-2015, the average abundances of the total phytoplankton, diatoms, and dinoflagellates were 140×10⁴ ind/m³, 132×10⁴ ind/m³, and 8.4×10⁴ ind/m³, respectively, which had 6.0, 6.1, and 4.7 times increase compared to 1985-2000. In the Northern Yellow Sea, their abundances were 134×10⁴ ind/m³, 121×10⁴ ind/m³, and 12.9×10⁴ ind/m³, while in the Southern Yellow Sea they were 145×10⁴ ind/m³, 140×10⁴ ind/m³, and 5.1×10⁴ ind/m³, respectively. There was a dramatic increase in the dinoflagellate abundance and the ratio of dinoflagellates to diatoms increased by 1.13 times when compared to 1985-2000. In addition, this ratio had marked seasonality, with 7.29 times increase during the summer seasons compared to the other seasons. The average abundances of Noctiluca scintillans were 189×10³ ind/m³, 29.6×10³ ind/m³, 126×10³ ind/m³, 63.3×10³ ind/m³, and 3.19×10³ ind/m³, which had increases 11, 3.24, 11.5, 4.7, and 1.54 times, respectively, during 2005-2015. Similarly, in 2005-2015, the phytoplankton species richness in the Yellow Sea increased by 78.9%. The species diversity was maintained in the Northern Yellow Sea, while it increased by 28.9% in the Southern Yellow Sea, compared to 1985-2000. The long-term variations in the phytoplankton communities determine the variability in the diet composition and food basis of fishery resources. Research found that the fishery community structures had gradually declined with smaller sizes, low commercial value species, and young individuals in the catches. This is in conjunction with human fishing activities, environmental variability, as well as diets for the food base. From the perspective of the phytoplankton diets, this research provides basic data and references for further discussing the effects of phytoplankton changes on the ecosystem food web structure and early recruitment of fishery resources in the crucial habitats of the important fisheries in the Yellow Sea.