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The flooding process is one of the main concerns of damaged ship stability. This paper combines the volume of fluid (VOF) method incorporated in the Navier-Stokes (NS) solver with dynamic mesh techniques to simulate the flooding of a damaged ship. The VOF method is used to capture the fluid interface, while the dynamic mesh techniques are applied to update the mesh as a result of transient ship motions. The time-domain flooding processes of a damaged barge and a rectangular cabin model are carried out based on the abovementioned method, and the computational results appear compatible with the experimental data. During the flooding process, the motion of the flooding flow at different stages is observed and compared with that observed in real conditions. The time-domain research of the flooding process is the starting point for subsequent establishment of damaged ship’s roll movement and capsizing the mechanism of dead ship condition in wave.