Phytoplankton, as the leading primary producer in the water, is an essential component of the aquatic ecosystem and has a significant indicative effect on changes in the aquatic environment. The aquatic ecosystems of plateau oligotrophic deepwater lakes are more fragile, and the phytoplankton in the lakes are more sensitive to changes in the environment. To investigate the spatial and temporal characteristics of the phytoplankton community structure in Lake Lugu, a typical oligotrophic deepwater lake in Yunnan-Guizhou Plateau, and its relationship with environmental factors, the present study investigated the physicochemical properties of the lake water and the phytoplankton species, cell densities, and community structure in the lake of Caohai, Puluo Village, Luoshui Village, Dazu Village, and the Goddess Bay under five land-use types in four seasons of 2023, respectively. The results showed that the water of Lake Lugu as a whole was in a nutrient-poor state, and the concentration of nutrient, such as total phosphorus (TP), total nitrogen (TN), and nitrate nitrogen (NO₃-N) in the Caohai near the shore of the wetland was significantly higher than that in the other lake areas. A total of 119 phytoplankton was identified in 8 phyla, and the Bacillariophyta had the highest number of species and cell density. The dominant species of phytoplankton were 15 species from 5 phyla, dominated by Bacillariophyta and Cyanophyta; among them, Fragilaria sp. was the key dominant species in spring and autumn, and Dinobryon sp. was the key dominant species in summer. The Shannon-Wiener diversity index, Margalef richness index, Simpson dominance index, and Pielou evenness index of the phytoplankton communities in each lake area were generally low, indicating that the structure of the phytoplankton community in Lake Lugu is relatively simple, and the resistance to external and internal environmental changes is weaker. Pearson's correlation analysis indicated that the main environmental influence factors of chlorophyll-a and phytoplankton cell density were TN, TP and NO₃-N, and redundancy analysis indicated that the main environmental drivers of key dominant species of phytoplankton were water temperature, TN, NO₃-N, NH₃-N and DP, while Mantel test analysis showed that Shannon-Wiener diversity index, Margalef richness index and Pielou evenness index were highly significant or significantly positively correlated with TN, NO₃-N, and DP, respectively. In summary, NO₃-N, TN, TP, and DP may play a key role in driving the changes in phytoplankton biomass and community structure in Lake Lugu. This study revealed the spatial and temporal distribution characteristics and driving factors of the phytoplankton community in Lake Lugu, a typical plateau oligotrophic deepwater lake, under different land uses, which can provide scientific support for the protection and management of this type of lake.