Microcystis, one of the common cyanobacteria, often causes blooms in reservoirs, which has seriously threatened the safety of drinking water worldwide. To identify the growth characteristic of total and microcystin-producing Microcystis in large deep reservoirs, we used Quantitative PCR (qPCR) to measure the cell density of total and microcystin-producing Microcystis and monitored water quality in the water samples collected in Dongzhang Reservoir once a month. Microcystis blooms occurred in Dongzhang Reservoir in April 2017, which was composed of microcystin-producing and non-microcystin-producing Microcystis. Water temperature, dissolved oxygen, pH, and chlorophyll-a showed significant vertical stratification during Microcystis blooms. Total and microcystin-producing Microcystis grew rapidly under the high concentration of total phosphorus and rising water temperatures. Nitrate-nitrogen had a significant linear correlation with the abundance of microcystin-producing Microcystis. Our results indicated that nutrients and water temperature could be key triggers of Microcystis blooms and nitrate-nitrogen potentially regulates the competition between microcystin-producing and non-microcystin-producing Microcystis. This study improves our understanding of the characteristics of Microcystis blooms and the competition between microcystin-producing and non-microcystin-producing Microcystis in large deep reservoirs.