Heavy metal pollution induced by human activities is widely regarded as a major environmental stressor for many lakes. Yangzong Lake, one of the nine largest plateau lakes in Yunnan Province, has experienced severe arsenic contamination since 2008. Monitoring data further showed that lake-water arsenic concentration consistently exceeded the standards for drinking water quality, posing severe risk for water safety and ecosystem health. A spatial survey and analysis of surface water quality and phytoplankton in Yangzong Lake was conducted bimonthly from April 2015 to February 2016, covering the south, central and north parts of the lake basin, respectively. A total of 68 algal taxa were identified, with the largest number of taxa belonging to Chlorophyta. However, Cyanophyta was absolutely dominant throughout the study period, and consisted of Pseudoanabaena, Planktothrix and Aphanizomenon. These results were consistent with previous surveys of phytoplankton from this lake, confirming the cyanobacteria-dominated community structure after the occurrence of arsenic pollution. The analysis of variance demonstrated that the phytoplankton biomass exhibited a significant seasonal fluctuation, with a maximum value found in August (14.06 mg/L) and a minimum biomass occurring in December (1.23 mg/L), while no significant spatial variation was observed. The Pearson correlation analysis showed that phytoplankton total biomass was significantly and positively correlated with water temperature and pH, but negatively correlated with arsenic concentration, water transparency, manganese concentration, sodium concentration, potassium concentration and total phosphorus concentration. Redundancy analysis displayed that water temperature, arsenic concentration, calcium concentration, manganese concentration and potassium concentration altogether accounted for 57.18% of the community variation in Yangzong Lake. The variation partitioning further showed that the water temperature, calcium concentration and arsenic concentration accounted for 32.05% of the spatio-temporal variation of phytoplankton community in Yangzong Lake, while the water temperature, calcium concentration and arsenic concentration independently accounted for 12.45%, 8.28% and 2.33% of the total variance, respectively. The coupling of arsenic concentration and water temperature explained 9.46% of the community variation. Therefore, we infer that seasonal fluctuation of water temperature may have caused the change in lake stratification and the increased water mixing under lower temperature may promote the sediment release of arsenic, resulting in higher lake-water arsenic concentration and stronger community turnover of phytoplankton. This study will help to evaluate the long term ecological effect of heavy metals on lakes and provide scientific evidence for restoration of arsenic polluted plateau lakes.