In view of the problems existing in the traditional rule-based control methods in the control of green heating systems with heat pump units as the main equipment, such as high operating costs, poor user thermal experience, and adverse impact on equipment service life, this study proposes a multi-objective optimal regulation method based on the NSGA-II algorithm. The method takes economy and thermal comfort as the optimization goals, considers the influence of different outdoor temperatures on user-side heat load demand, building heat loss and heat pump energy efficiency, and dynamically adjusts the output of heat pump equipment and the opening degree of user-side valves under changing outdoor environments, thereby meeting the requirements of different index weights set by users and ensuring the economical and efficient operation of the system. Experiment results show that: the control method proposed in this paper can dynamically adjust the optimal output strategy of the equipment according to the different requirements of the user; compared with the traditional control method, under the same comfort weight requirements, the optimization method reduces the total power consumption of the heat pump unit by 5.85% while the thermal comfort indexes deviate from the optimal value by 19.85%. In addition, the frequency and magnitude of power fluctuations of the heat pump are significantly reduced, which also improves the safety and lifetime of the equipment. The optimal regulation strategy proposed in this paper has better economy, thermal comfort and stability, and can provide an optimized reference for the control of similar green heating systems.