Passive safety system is extensively employed in newly designed reactors to increase their inherent safety. However, the driving force is smaller, and the uncertainty of the thermal–hydraulic (T-H) process may potentially result in the inability of system to perform its intended function, which is often known as functional failure. Therefore, the passive systems reliability has received increasing attention. Unfortunately, the assessment of system failure probability utilizing Monte Carlo simulation (MCS) methods necessitates a significant quantity of repeated calculations employing the thermal–hydraulic code, which may be impractical in terms of computational cost. To enhance the assessment calculation efficiency, an adaptive surrogate model is proposed. The bootstrap method was employed to introduce an error estimate into the polynomial chaos expansion (PCE) model, which solves the obstacle of the PCE model in reliability evaluation applications due to the lack of error estimation. The method constructs an active learning approach through error estimation, strategically identifies and selects the best candidate samples, and iteratively updates the initial experimental design. The effectiveness of the method was verified through three benchmark cases, and it was employed for assessing the passive residual heat removal system (PRHRS) reliability within integral-type pressurized water reactor (IPWR200). The results demonstrated that the proposed method significantly diminishes the frequency of invocations to the T-H code and improves computational efficiency to a large extent. Furthermore, it can serve as a valuable guide for the design, operation, and reliability evaluation of the passive system.