Natural circulation in the lead–bismuth reactor is important to remove heat from reactor core under normal and accident conditions. In this study, experimental and modeling test study was conducted on the non-nuclear integrated China Lead-alloy Cooled Reactor (CLEAR-S) test facility to investigate the natural circulation characteristics of Lead–bismuth for LBE-cooled reactor. A thermal–hydraulic analysis model suitable for the simulation of transient process of natural circulation of lead–bismuth is established based on the thermal–hydraulic physical models of main components in the primary and the secondary loops of the CLEAR-S facility, such as the core, the main pump, the main heat exchanger (MHX), and the decay heat removal heat exchanger (DHR), pipes, valves and so on. Based on the experiments’ data obtained under different power levels, the thermal–hydraulic modeling of the CLEAR-S system was verified. The results show that there is an acceptable agreement between the model and experiment and the transient process of natural circulation can be well simulated. A prediction model adapted to the temperature distribution of the whole primary loop in the CLEAR-S reactor is established in this paper. This study can support the analysis of natural circulation during the development of lead–bismuth reactors.