Abstract: Because of the discontinuous change in the compressibility between a two-phase mixture with a small void fraction and the pure liquid phase and the discrete method of the discrete momentum equation, the thermal hydraulic system program based on the two-fluid six-equation method may calculate a fictitious pressure peak when the steam is about to disappear from the volume or the water is about to fill the volume. In this paper, the thermal hydraulic system analysis program RELAP5 is used as a reference to analyze and mitigate the water packing problem. The detailed detection logic and mitigation scheme are given, and applied in the calculation and analysis of the Pryor’s Pipe Problem and the Condensation Test. The results show that the implementation of the water packing mitigation scheme can alleviate the pressure transient effects caused by the numerical method in the two-fluid program, which can significantly reduce the pressure peaks and avoid the emergence of severely distorted transient solutions. The water packing mitigation scheme slows down the peak of this fictitious pressure, which is helpful to improve the stability of program calculation. In view of this problem, this method can provide a reference for the development of the same type of system program and model optimization.