The invention discloses a simulation system for algal bloom emergency regulation and control under a changing environment and a method of the simulation system. The simulation system comprises a water customizing unit, a multifunctional simulation unit, an environment regulation unit, an algal bloom charging unit, a water quality monitoring unit and a control platform, wherein the water customizing unit is used for treating and customizing source water into experimental water, the multifunction simulation unit physically models according to a large-scale water area and simulates an algal bloom emergency measure, the environment regulation unit is used for emulating combined changes of field environment conditions, such as illumination, temperature and wind field, the algal bloom charging unit realizes spatial distribution simulation of algal blooms in any form at any time, the water quality monitoring unit is used for measuring spatial and temporal distribution of key water quality indexes in real time, and the control platform is used for controlling an operation state of a key device. The simulation system for the algal bloom emergency regulation and control under the changing environment and the operation method of the simulation system are suitable for prediction and optimization of emergency disposal scheme effects after large-scale water area algal bloom breaks out, and can conveniently and accurately predict implementation effects of algal bloom emergency measures, such as drainage basin water transfer, local water circulation and aeration methods.