With the development of aerospace technology, many devices under test (DUTs) in thermal vacuum tests require balanced heating. However, traditional PID controllers mostly focus on single-channel independent control, lacking effective solutions for the mutual influence among multiple channels. This paper proposes a PID controller based on average temperature feedback to address the issue of temperature imbalance in multi-channel heating. Firstly, this method calculates the difference between each channel’s temperature and the average of all channels’ temperature, and then feeds the difference into the input of the PID controller to real-time adjust the heating rates for each channel, ensuring balanced overall heating. Secondly, by detecting whether each channel has reached the lower limit of the set temperature range, the opportunity to exit the average temperature feedback is provided. Finally, a temperature acquisition and control synchronization system based on the EtherCAT network was built, providing an experimental platform for validating the proposed method. Through simulation and experimental validation, the proposed method not only reduces temperature difference among channels during the heating process, but also enhances the overall stability and robustness of the system. This makes it an effective solution for achieving precise thermal control in complex multi-channel environments.