Abstract: Sampling and monitoring were conducted annually (from February 2012 to March 2013) in four different water areas (Jiangdong, Balongdao, Shangyintun, Handa), and grey correlation analysis was carried out between phytoplankton diversity (H) and environmental factors. The theoretical reference for the reasonable development and utilization of water resource of different reservoirs was provided through the research of Yantan reservoirs on the main ecological environmental factors including phytoplankon diversity and its efficiency. The results showed that Yantan reservoir (each monitor water area) phytoplankton Shannnon-Wiener diversity index (H) was 1.39-3.17, the level changed by Shangyintun (fenced culture area)> Handa (main channel non-culture areas)> Balongdao (cage culture inferior intensive area)> Jiangdong (cage culture intensive area). In monitoring factors, water temperature had the highest correlation with phytoplankton diversity and the association degree was 0.774, secondly, the pH, CODMn and NO2-N were respectively 0.685, 0.628 and 0.578. TP and BOD5 had relatively less effect on planktonic community structure, the association degrees were respectively 0.498 and 0.354. Due to relatively intensive fish cage culture, particular cultured area phytoplankton species (genus) density and biomass increased, while level of biological diversity (H) decreased.