Abstract: The pipe filling process of cryogenic propellant pipelines could result in severe water hammer damage, and the formation mechanism and evolution exhibit significant differences compared to the water hammer in room-temperature condition. A Computational Fluid Dynamics （CFD） model for the cryogenic liquid filling a room-temperature pipeline was established, which enables coupled calculations of large temperature heat transfer, gas-liquid mixing, and phase change effects. The model provides insights into the two-phase flow patterns, heat and mass transfer, and the pressure transient variation in the cryogenic filling process. It was found that the water hammer induced by cryogenic filling could be divided into four stages, including the gas compression, the condensation induced water hammer, the oscillatory decay, and the stable evaporation. The pressure peak value in the cryogenic filling event owned to two mechanisms, involving the inertial flow cut-off of liquid flow and the condensation water hammer of cavitation, and the cavitation condensation effect played the dominant role in the cryogenic condition. Compared to the room-temperature liquid filling situation, the gas-liquid phase transition results in higher water hammer pressure amplitude and faster pressure decay during a cryogenic pipe-filling process. When the evaporation and condensation is neglected, nitrogen gas inside the pipeline is compressed under the inertial impact of liquid nitrogen, and liquid nitrogen's kinetic energy is gradually released, resulting in lower acceleration(354 m/s²) and lower pressure fluctuation. However, when gas condensation effects become significant, the nitrogen gas inside the pipeline essentially liquefies during the liquid nitrogen filling process, losing its buffering effect. This leads to a severe flow cutoff phenomenon in the liquid nitrogen, with acceleration reaching up to 1102 m/s² and an increase in impact pressure. When the container pressure was 0.2 MPa, the maximum pressure at the end of the pipeline could reach about 0.843 MPa.