Scientific experimental racks are an indispensable supporter in space stations for experiments with regard to meeting different temperature and humidity requirements. The diversity of experiments brings enormous challenges to the thermal control system of racks. This paper presents an indirect coupling thermal control single-phase fluid loop system for scientific experimental racks, along with fuzzy incremental control strategies. A dynamic model of the thermal control system is built, and three control strategies for it, with different inputs and outputs, are simulated. A comparison of the calculated results showed that pump speed and outlet temperature of the cold plate branch are, respectively, the best choice for the control variable and controlled variable in the controller. It showed that an indirect coupling thermal control fluid loop system with a fuzzy incremental controller is feasible for the thermal control of scientific experimental racks in space stations.