Sensitivity analysis is applied to uncertainty analysis and reliability evaluation of the thermal-hydraulic process for reactor passive system, which can quantitatively identify uncertainty input parameters that have important influence on system’s thermal-hydraulic behavior. Based on hybrid of random balance designs and Fourier amplitudes sensitivity test (HFR), the passive residual heat removal experimental system of a nuclear power plant is used as an example to carry out the global sensitivity analysis. The applicability and accuracy of HFR method are demonstrated by simulation results. The change rule of parameter importance with time and the parameter importance ranking when the system is running stably are given by sensitivity analysis, which help to guide passive system’s design optimization and operation management.