The harmful cyanobacteria pose a serious threat to the safety of drinking water sources because of their ability to release microcystins (MCs). To illuminate the status of MCs contamination and the effect of its variants composition on water quality in Lake Chaohu, the temporal and spatial distribution of intracellular microcystins (IMCs) and extracellular microcystins (EMCs) and main environmental factors in this lake were examined in summer (August) and autumn (November) of 2012, winter (February) and spring (May) of 2013, respectively. The results showed that the average concentrations of IMCs and EMCs varied from 0.12 to 6.45 μg/L and from 0.69 to 1.92 μg/L, respectively. Among the three common variants, the proportions of MC-LR and MC-RR to total MCs were higher, and the MC-YR was the lowest. MC-RR and MC-LR were the major MCs variants in Lake Chaohu. The concentration and proportion of IMCs and EMCs variants showed different temporal and spatial distribution characteristics. Statistical analysis showed that Microsystis biomass, water temperature, total phosphorus were the key environmental factors affecting the variation in concentration and composition of different MCs variants. This study highlight the fact that the more MC-RR variant can be synthesized in the western Lake with high eutrophication in summer, while more toxic MC-LR variant was released into water in autumn and winter. Understanding the changes of MCs variants composition and its key factors can help to predict the contaminative status of MCs and assess the risk of MCs in drinking water sources.