The sterilization of liquid eggs plays a crucial role in the production of liquid egg products. Traditional pasteurization techniques can easily cause protein denaturation, while non-thermal sterilization techniques are often constrained by processing intensity and time. Improving the effectiveness of liquid egg sterilization while preserving the stability of its functional attributes poses a significant challenge. In response to this issue, a synergistic ultrasonic mild thermal sterilization system for liquid eggs is proposed, accompanied by the optimization of its process parameters. COMSOL is employed to simulate the acoustic field distribution of the ultrasonic–thermal system in the liquid egg medium. Verification is conducted through acoustic intensity measurements, and analysis is performed to obtain the optimal arrangement of ultrasonic transducers. Based on Modbus communication, an ultrasonic–thermal synergistic sterilization system is designed. Sterilization experiments are conducted with both 20 kHz + 28 kHz and 20 kHz + 40 kHz multifrequency ultrasound, compared with traditional 20 kHz single-frequency ultrasound. The results indicate that multifrequency ultrasound improves sterilization efficiency by approximately 15% compared to traditional single-source ultrasound. Utilizing multifrequency ultrasonic–thermal synergistic sterilization experiments, a three-factor, three-level response surface test is conducted with sterilization rate and foaming properties as evaluation criteria. The results indicate a strong correlation between ultrasonic frequency, processing time, heating temperature, and sterilization performance, with the impact magnitude being sterilization temperature > processing time > ultrasound frequency. Parameter optimization analysis is performed using a genetic algorithm, yielding sterilization conditions of 55 °C, 11 min and 30 s processing time, and 20 + 40 kHz ultrasonic frequency. The liquid egg sterilization rate is 99.32%, an average decimal reduction of 3.17 log values, and foaming properties are 42.79%.Through comparative analysis, it is determined that the sterilization rate of the ultrasonic–thermal synergistic sterilization system meets national standards, and functional properties such as foaming are superior to traditional pasteurization. This validates the proposed ultrasonic–thermal synergistic liquid egg sterilization control system as effective and feasible.