In the process of frozen food production, its refrigeration system is a typical large inertia, nonlinear, strongly coupled system, which is prone to large overshooting during operation, resulting in cost increase and quality control problems. This paper solves the problem of large overshoot in the digital PID control process by designing a fuzzy control, and designs a practical fuzzy controller so that the design method of the fuzzy PID controller can be realized in the simulation and actual control of the freezing system. A genetic algorithm optimization scheme is also designed for the fuzzy PID control system to optimize the fuzzy controller’s affiliation function, control rules, as well as proportionality and quantization factors, to enhance the model’s dynamic characteristics and robustness. Design of food quick-freezing simulation experiments and use the model in the refrigeration system control in practice, compare the performance of this model with the PID, fuzzy PID model, and found that the temperature difference set value of 4 ℃ and 3 ℃, respectively, the parameters of the traditional PID controller in the commissioning stage of the system after the end of the rectification to remain fixed, which makes the actual quality of the cooling water temperature difference control degradation. And the fuzzy genetic PID controller still has good control quality. In this paper, the model curve converges rapidly, the overshoot is only 3.9%, and the regulation time is only 450M seconds. The designed method of the study is feasible and has high industrial application value.