To characterize the ultraphytoplankton community structure and understand its succession and its relationship with environmental factors, High Performance Liquid Chromatography (HPLC -CHEMTAX) was used to analyze the photosynthetic pigment concentration and the algae composition. Algal phyla composition and their abundance were determined based on the presence of pigments, and environmental parameters were synchronously tested in the Three Gorges Reservoir in China. Highperformance liquid chromatography (HPLC) analysis showed that there were eight characteristic photosynthetic pigments in the Three Gorges reservoir area: alloxanthin, chlorophyll b, chlorophyll a, fucoxanthin, lutein, neoxanthin, violaxanthin, and zeaxanthin. Among them, fucoxanthin, allophycocyanin, zeaxanthin, and chlorophyll b were the most important photosynthetic pigments in the Three Gorges reservoir area. There were significant differences in the time scale of the eight photosynthetic pigments (P < 0.05), but no significant difference in the seven phyla (P > 0.05). The calculation of the matrix factorization program chemical taxonomy (CHEMTAX) showed that the ultraphytoplankton community was composed of 7 phyla: Euglenophytes, Chrysophytes, Cyanophytes, Cryptophytes, Chlorophytes, Diatoms, and Dinoflagellates. Redundancy analysis (RDA) revealed that the key environmental factors that affected the structure of the ultraphytoplankton community were light intensity, total phosphorus, and water temperature. The results provided a basis and data support for the biodiversity of phytoplankton in the Three Gorges Reservoir and its relationship with environmental factors and environmental monitoring.