In recent years, computer technology has entered a period of rapid development, and it has become more and more important to use water ecological models to simulate the ecological changes of water bodies and the impact of pollutants on ecosystems. The purpose of this paper is to study phytoplankton community characteristics based on ecological simulation. Firstly, the principle and main simulation process of the AQUATOX model are expounded in detail, and then on the basis of collecting the data of various water quality indicators and phytoplankton measured in M Lake, the model simulation area and parameters are determined, and the M Lake ecological model is established. The model was used to simulate the seasonal succession law of three kinds of large aquatic plants (Eyes serrata, algae, chara) and three kinds of algae (cyanobacteria, green algae, diatoms) and the change law of the main zooplankton in the lake area, In the simulation of aquatic plant and algal biomass in the lake area, it is found that the simulation effect of green algae and cyanobacteria is better, and the average relative error is within 20%, while the average relative error of diatom simulation is larger, which is 30%.