As the second deepest lake in China, Lake Fuxian is one of the most important storages of the national strategic freshwater resources. With the intensification of climate change and catchment development, biological communities in Lake Fuxian had changed obviously in recent years with the deterioration of water quality and lake ecosystem health. We conducted a monthly survey of three sampling sites covering the south, central and north parts of the Lake Fuxian Basin in 2015 to identify the spatiotemporal pattern of phytoplankton communities and their environmental drivers. Our results showed that the phytoplankton community was composed of Chlorophyta, Pyrrophyta, Chrysophyta, Bacillariophyta, Cyanophyta and Cryptophyta, and there were strong seasonal fluctuations in biomass and community structure but no significant spatial variation was observed. The dominant taxa were Aphanocapsa sp., Ulothrix sp. and Mougeotia sp. (January), Fragilaria crotonensis, Ceratium hirundinella and Mougeotia sp. (February), Cyclotella spp. and Mougeotia sp. (March), Dinobryon spp., C. hirundinella and Mougeotia sp. (April-July), C. hirundinella and Mougeotia sp. (August), C. hirundinella, Dinobryon spp. and Mougeotia sp. (September), C. hirundinella (October), C. hirundinella, Peridinium sp. and Mougeotia sp. (November), Mougeotia sp. (December), respectively. Multivariate analyses showed that temperature and total phosphorus were significant factors in driving phytoplankton community structure, in accounting for 26.0% and 2.6% of the total variance independently with a shared portion of 3.0%. When compared to the predominance of Mougeotia sp. as surveyed in 2002-2003, there exists a significant change in phytoplankton communities with an obvious increase in algal biomass in 2015, which was likely linked to the long-term increase of lake nutrient levels.