The permeability coefficient determines the estimation of water inflow at deep foundation pits and the type of the water cutting-off curtain, and affects the safety and cost of the project; thus, it is of great significance to the construction of deep foundation pits in water-rich areas. For anisotropic aquifers, it is difficult to find a suitable method to calculate the hydrogeological parameters from the existing analytical formula, especially for the vertical permeability coefficient. A pumping test was carried out on the flow resistance by using the temporary water cutting-off curtain in the field to simulate the dewatering of foundation pits; then, the hydrogeological conceptual model and the groundwater flow mathematical model were established to invert the permeability coefficient of each layer by using a 3D finite difference numerical simulation software; finally, the model was validated by the data of verification pumping; which provided a guiding basis for the design of the envelope of a subway station in the super-thick sand and gravel stratum near the river in Fuzhou. The results of the test and the numerical simulation can be used for reference for similar projects.