An efficient and reliable spacecraft payload thermal management method is one of the key problems to build China Space Station (CSS). Aiming at the outstanding characteristics and difficulties of the payloads rack in the experimental lab module of CSS, in the aspects of thermal control interface, boundary constraint, scale quantity, space layout, diversity of temperature control, operation mode and working life, etc., a two-stage thermal management scheme based on single-phase fluid loop is proposed and constructed. A fluid drive unit is designed to drive the fluid circulation and health management of the module thermal control bus (TCB). In view of the different characteristics of the payload racks, three different types of second-stage thermal control systems are proposed, and different thermal control terminals are designed, in order to solve the problem of thermal control resource allocation and health management in payload racks. A method based on “pump bypass” and “valve resistance ratio” is used to control the flow rate of the thermal management system. Based on the overall scheme of the thermal management system and the developed flight products, on-orbit verification and data analysis are carried out. Flight verification shows that the key parameters of the fluid loop in the thermal management system on orbit are basically consistent with the ground data; the maximum deviation is 1.84%. The pressure control accuracy of the bypass system reaches ±2%, and the active heat transfer efficiency of the integrated thermal management system is over 83%, which can effectively meet the thermal control requirements of the two-stage payloads in the module and rack. After on-orbit flight verification, the designed thermal control system works well on orbit and exhibits good stability.