Abstract: Phytoplankton is the most important biological component in the reservoir ecosystem, which could indicate the status of aquatic ecosystem due to its sensitive to environmental variation. To understand the application and difference between two methods of phytoplankton functional group classification, functional groups (FG) and morphology-based functional groups (MBFG), in indicating the changes of reservoir environment, we investigated water quality and phytoplankton in Qingshitan Reservoir monthly from March 2016 to February 2017. Two phytoplankton functional groups classifications (FG and MBFG) were used to analyze phytoplankton community composition, seasonal succession, and its driving factors. We compared the application and differences of two methods of functional group classifications in indicating environmental changes. The results showed that there were 109 species belonged to seven phylum, which could be classified into 17 FG or 5 MBFG functional groups. Results from both methods indicated that the reservoir was meso-eutrophic. The phytoplankton seasonal succession under 8 or 9 steps with FG or 8 steps with MBFG. Results from the redundancy analysis showed that the response of phytoplankton community reflected with FG to environmental variation was more sensitive than that with MBFG, especially in the response to the changes of pH and nitrate concentration. In conclusion, FG was more appropriate in describing community succession and exploring the relationship between phytoplankton and environment.