To understand the succession characteristics and driving mechanism of phytoplankton community structure in large reservoirs, the Xin'anjiang Reservoir (Qiandaohu Reservoir) in Qiantang River Basin was chosen as the case study. From 2002 to 2017, the surveyed phytoplankton data, physicochemical variables and hydro-meteorological conditions were investigated to understand long-term variations of phytoplankton community and dominant genus, therefore to discover the main factors driving changes of phytoplankton community structure. The results showed that from 2002 to 2017, 7 phyla including 93 genera of phytoplankton were existed in Qiandaohu Reservoir, which were mainly composed of Bacillariophyta, Chlorophyta, Cyanophyta and Cryptophyta. In the past 16 years, annual abundance and community structure of phytoplankton experienced four stages:before 2008, the abundance of phytoplankton cell maintained at a low level and cyanobacteria was not the main group. During 2009 and 2012, the cell abundance of phytoplankton was at a high level with cyanobacteria becoming the main group. The cell abundance of phytoplankton and proportion of Cyanophyta decreased during 2013 and 2015. Phytoplankton cell abundance increased during 2016 and 2017 with cyanobacteria becoming the main group again. When the phytoplankton changed, the dominant genus also changed. The phytoplankton dominant genus were Cyclotella, Cryptomonas and Chroomonas from 2002 to 2008, then changed to Oscillatoria, Chlorella, Cyclotella and Chroomonas during 2009 and 2012, and turned Anabaena, Aphanizomenon, Cyclotella, Synedra, Melosira, Scenedesmus and Chroomonas during 2013 and 2017 at last. RDA analysis showed that hydro-meteorological factors such as temperature, wind speed, water level and inflow, and water quality factors such as total nitrogen, conductivity, nitrogen-phosphorus ratio and transparency were significantly related to phytoplankton community structure. The results show that in oligotrophic and mesotrophic reservoirs such as Qiandaohu Reservoir, the phytoplankton community structure was not only affected by the nutrients, but also strongly affected by hydro-meteorological conditions. This complex relationship poses a giant challenge to the ecological risks prediction of reservoir algal blooms and water quality management.