As an important central city in the eastern region of China, the subway lines are well developed in Nanjing, especially with densely distributed stations in the polder areas on both sides of the Yangtze River. The waterlogging level in the polder area is an important factor affecting the layout, design and construction of subway stations. Taking a polder area where the Nanjing subway station is located as an example, the measured terrain elevation data is imported into ArcMap for triangular grid differential processing to generate the relationship between water level and storage volume in the polder area. Through the investigation of the relationship between water level and storage capacity of the waterlogging quantity calculated by hydrologic method, the waterlogging water level in the polder area under the subway design standard is obtained. The result shows that this method can really reflect the terrain features in polder areas, which provides a good data base for calculation of waterlogging level. The relationship between the water level and water storage is rapidly calculated to avoid the calculation error of waterlogging level recommended by manual drawing contour line. The accuracy and efficiency of calculating the waterlogging level are improved, which can provide the reference for similar work in the future.