Microwave heating inhomogeneity has always been a hot issue in microwave heating control research. According to the physical structure of the microwave heating device, the static difference model of the surface temperature of each layer in the furnace is established, and the actual power of microwave heating is obtained by combining with experiments. Based on the finite difference method of heat transfer, the temperature distribution model in 3D space is established, and the effectiveness of the model is verified by MATLAB and COMSOL simulations. The equilibrium temperature of the heated medium obtained by uniformly heating the microwave is compared with the temperature distribution during uneven heating, the partial temperature rise equilibrium points of the medium during the microwave heating process are identified. Finally, comparison is carried out to find out the best point for the control object for expert PID (proportion-integral-derivative) microwave heating. The experimental results show that this method can accurately measure the equilibrium temperature of liquid heated medium at any time, and can make microwave heating more widely used in industrial production.