Payload racks are designed to provide common interfaces for users on the Space Station. Thermal control system is necessary for payload rack to prevent equipment from overheat. A feasible control strategy, using temperature difference of inlet and outlet as the feedback variable for water-cooled branch, and percentage of the heat dissipation by air accounting for the total heat dissipation (water and air) as the feedback variable for air-cooled branch, is proposed in this paper. The working principle of the fuzzy incremental control algorithm (FIC) is introduced and applied in the thermal control system. The thermo-hydraulic model of rack with combination of air-cooling and water-cooling is also presented in this paper. The dynamic response of the control system is investigated by simulation. The simulation results show that FIC takes advantages of no steady error, small overshoot and fast response. The control strategy is demonstrated to be effective, stable and of high accuracy.