With the development of society and economy, impervious structures such as buildings and hardened pavement gradually replace a large number of original natural ground, resulting in a rapid reduction of rain infiltration area and urban waterlogging. In order to solve the dual hazards of water shortage and seasonal urban flood in China, a vertical seepage device with sand and aggregate as internal material in clay layer was proposed. When heavy rainfall occurs, surface runoff will converge in densely packed sand seepage wells, and then seep along the wellbore into the surrounding soils. Because the area of shaft lining is much larger than that of wellhead, and the horizontal permeability of clay is generally greater than its vertical permeability, sand and stone seepage wells can greatly increase the infiltration rate of rain water. The permeability of sand and stone seepage wells with filling materials and geotechnical media was tested, based on which, the in-situ test and numerical simulation of single and group wells are established. The results showed that the device is economical, simple and effective, and it is an environment-friendly and low-impact sponge city construction method, which provides an effective way for the construction of sponge city in clay areas.