Our investigation in 2007 revealed that the concentration of microcystin (MC-LR) in Miyun reservoir was 0.224 μg L-1, below the safety limit of surface drinking water in China (1.0 μg L-1). The phytoplankton community in Miyun reservoir was composed of 8 divisions and 84 species (including genera and varieties). The density of phytoplangkton was 393.71?—104 cells L-1 including 24.6% of Chlorophyta, 32.5% of Cyanophyta and 15.3% of Bacillariophyta. The toxin-producing cyanobacteria included Microcystis sp., Oscillatoria sp. and Anabaenopsis sp. The MC-LR content was positively correlated with the toxic cyanobacterial density. Total phosphorus (TP), total nitrogen (TN), transparency (SD), CODMn had reached the level of mesotrophy. Nitrogen source and organic pollution had been on the rise. Correlation analysis and cluster analysis showed that NH4-N, TP, NO3-N and TN might affect the biosynthesis of MC-LR directly. Therefore, preventing and controlling water eutrophication is the key to maintain water supply safety in Miyun reservoir.