A radiant floor cooling system (RFCS) is a high-comfort and low energy consumption system suitable for residential buildings. Radiant floor systems usually work with fresh air, and their operating performance is affected by climatic conditions. Indoor and outdoor environmental disturbances and the system’s control strategy affect the indoor thermal comfort and energy efficiency of the system. Firstly, a multi-story residential building model was established in this study. Transient system simulation program was used to study the operation dynamics of three control strategies of the RFCS based on the calibrated model. Then, the performance of the control strategies in five climate zones in China were compared using multi-criteria decision-making in combination. The results show that control strategy has a negligible effect on condensation risk, but the thermal comfort and economic performance differ for different control strategies. The adaptability of different control strategies varies in different climate zones based on the consideration of multiple factors. The performance of the direct-ground cooling source system is better in Hot summer and warm winter zone. The variable air volume control strategy scores higher in Serve cold and Temperate zones, and the hours exceeding thermal comfort account for less than 3% of the total simulation period. Therefore, it is suggested to choose the RFCS control strategy for residential buildings according to the climate zone characteristics, to increase the energy savings. Our results provide a reliable reference for implementing RFCSs in residential buildings.