Qingcaosha Reservoir located at Yangtze Estuary of China is a newly constructed and one of the largest tidal reservoirs in the world, which will be an important drinking water source of Shanghai. This study aims at investigating microbial community and its shifts corresponding to different water quality during the test running period of Qingcaosha Reservoir. The results showed lower concentrations of total nitrogen (TN) and total phosphorus (TP) in the reservoir than that in Yangtze Estuary. The number of total cultivable bacteria was significantly lower in the reservoir than that of Yangtze Estuary. The denaturing gradient gel electrophoresis (DGGE) analysis showed that the dominant microbes were alpha-Proteobacteria, beta-Proteobacteria, Flavobacterium, Rheinheimera, Prochlorococcus, and Synechococcus. The quantitative PCR (q-PCR) results revealed significantly higher number of cyanobacteria and Microcystis in the reservoir during summer season. In addition, bacterial abundance positively correlated with TP concentration inside the reservoir. These results indicated that Qingcaosha Reservoir had ability to reduce the TN and TP in influent and improve the water quality overall. However, it also faced the risk of potential cyanobacteria bloom and eutrophication in Qingcaosha Reservoir where phosphorus will be the nutrient limiting factor.