HPR1000, as China’s completely independent intellectual property third-generation advanced nuclear technology, integrates both active and passive safety measures, making it one of the safest advanced nuclear technologies. In the technical features of HPR1000, the active safety system mainly addresses anticipated operational occurrences and design basis accidents, while the passive safety system is designed to respond to design extension conditions. Typical passive safety systems include the secondary side passive residual heat removal system (SPRHR), passive containment cooling system, and passive reactor cavity flooding system. Passive technology has advantages such as a simple structure, reduced human intervention, and less dependence on external electrical power or signals. However, in passive systems, the natural forces and resistances that drive the system are of similar magnitudes, and various uncertainties in physical processes that can be ignored in active systems become significant. The uncertainty in the physical processes involved is greater than in active systems, meaning that even when components function normally, the system may still fail to perform its expected safety functions, leading to failure of the system’s physical processes. This paper focuses on the SPRHR of HPR1000, establishes a physical model, and conducts reliability analysis using the RELAP5 code. The analysis investigates the failure mechanisms of physical processes under different accident conditions, considering parameters such as steam generator internal conditions, tank height, heat transfer area, and others that affect the operating characteristics of the system. The paper also evaluates the system’s functional reliability. The results show that the probability of physical process failure in the secondary passive residual heat removal system of HPR1000 is within an acceptable range, with no unacceptable risks identified.