Microcystis blooms occur frequently in subtropical lakes and reservoirs and cause serious ecological and economic losses. A novel Microcystis bloom caused by Microcystis densa has broken out in many reservoirs in South China. In order to control M. densa bloom, it is important to predict the growth of M. densa, which is influenced by the synergistic uptake and assimilation of nitrogen and phosphorus. Therefore, it is necessary to develop a model of the response of Microcystis growth to nitrogen and phosphorus concentrations. Our study focused on both nitrogen and phosphorus, and studied their synergetic effect on M. densa growth. The growth kinetics, including the maximum specific growth rates and the half-saturation constant of M. densa for both nitrogen and phosphorus, were also determined. A modified model with Monod kinetics was developed to explain the synergistic effects of nitrogen and phosphorus on M. densa growth. The specific growth rate of M. densa can be predicted by nitrogen and phosphorus concentrations. This modified model was verified by the actual measures of the Lianhe Reservoir and Liuxihe Reservoir. It could relatively accurately predict the growth level of M. densa and helped for the daily monitoring of reservoir management for M. densa growth.