With the comprehensive implementation of "deep earth exploration" in China, urban underground space development has been further improved, more and more environmental problems come with groundwater control in deep excavations. Especially in built-up areas, how to balance groundwater level on both sides of foundation pit and control ground settlement become a hot research topic. However, without the guidance of a perfect theoretical foundation, engineers can only explore some foundation pit dewatering design ideas based on personal experience. "Layered dewatering" was firstly put forward in the process of foundation pit dewatering on Yishan Road station of Shanghai Metro Line 9, when obviously hydraulic differences exist between layer ⑤3-2 (silty clay) and layer ⑦2 (fine sand). However, design concept of wells screen between two connected aquifers with difference hydraulic permeability is still unclear, and usually causes excessive exploitation of groundwater. In this paper, based on the analysis of shallow geological conditions in Shanghai, five kinds of combined strata with difference hydraulic permeability are summarized, and six dewatering design concepts are put forward. Based on the numerical simulation and comparison analysis of foundation pit dewatering design scheme on Biyun Road station of Shanghai Metro Line 14, the optimization design scheme of wells screen structure is put forward, and the total pumping volume of foundation pit is reduced by 13%.