The occurrence of extreme weather, such as heavy rainfall and sudden increases in precipitation, has led to a notable rise in the frequency of flooding in subway stations. By conducting numerical simulations of flood disasters in subway stations under heavy rainfall conditions and gaining insights into the patterns of flood invasion inside the stations, it is possible to develop practical and feasible drainage designs for the stations. This paper employs the computational fluid dynamics (CFD) method, utilising the volume of fluid function (VOF) method and the renormalization k-ε group model within the vortex viscosity model. The complete process of flood invasion into subway stations with varying water levels (1500 mm, 2000 mm, and 2450 mm) is modelled, and the distribution of floods at different times under varying operational conditions is analysed to identify the evolutionary patterns of station flood history. The simulation calculations yielded the mass flow rate time history curve at the tunnel entrance and exit, which was then subjected to an analysis of its development trend over time. The total accumulated water in the subway station is calculated by integrating the difference in mass flow rate between the entrance and the tunnel exit, using the mass flow rate curve. In conclusion, the paper proposes drainage measures that provide valuable insights into pumping strategies when floodwaters infiltrate subway stations. The results indicate that the speed of flood spreading in subway stations increases with higher groundwater levels, and that the mass flow rate of floodwater entering the tunnels increases over time, eventually reaching a stable state. It was observed that, at certain times, the mass flow rate of floodwater into the tunnels exhibited a linear relationship with time.