To provide reference for the protection and management of the ecological environment in the sea area around Qilianyu Island, the characteristics of phytoplankton communities and environmental conditions in this area were analyzed based on survey data of four voyages from 2018 to 2021. The results showed that 341 species of phytoplankton were identified from 111 genera of five phyla, with Bacillariophyta (69.21%) and Pyrrophyta (23.75%) as the major species. Phytoplankton abundance fluctuated in the range of (2.34–2841.16)×10³ cells/m³ , with the highest mean value in autumn 2018 (797.47×10³ cells/m³ ), followed by summer 2018 (675.40×10³ cells/m³ ), with the lowest value found in summer 2020 (91.39×10³ cells/m³ ). Phytoplankton abundance was mainly composed of Bacillariophyta (48.67%) and Cyanophyta (47.22%). Significant differences were observed in phytoplankton communities between the four periods (P=0.001). The diversity and evenness index of phytoplankton first increased and then decreased. The RDA analysis results showed that the main environmental factors affecting phytoplankton communities in Qilianyu Island were transparency, water depth, ammonia nitrogen, DIN, and N∶P with dominant factors changing in different periods. The nutrient factor limiting phytoplankton growth in this area changed from nitrogen to phosphorus. The decrease in phytoplankton diversity may be related to a nitrogen-phosphorus ratio imbalance caused by a surge of nitrogen content in the sea area. Therefore, the discharge of nitrogen-containing wastewater must be reduced and the protection and management of the ecological environment in the sea area must be strengthened.