For the comparison and selection of groundwater control scenarios for subway foundation pits in deep and high permeable aquifers, this paper presents the qualitative and quantitative comparison and selection framework of groundwater control scenarios for subway foundation pit by using analytic hierarchy process, fuzzy comprehensive evaluation method and numerical calculation method. A comprehensive comparison of various scenarios to groundwater control for a deep metro excavation in highly-permeable aquifers is established. Taking the foundation pit of Shuibu metro station in Fuzhou as an example, five different groundwater control scenarios (i.e. open dewatering, fully penetrating curtains, deep horizontal bottom sealing curtain, partially penetrating curtains with dewatering, underwater excavation) are evaluated and analyzed using proposed comparison method. The results show that the scenario of both partially penetrating curtains and dewatering is the best one for the groundwater control of the foundation pit of the station. Then, the numerical simulation method is used to analyze the surrounding surface settlement caused by foundation pit dewatering. The results show that the settlement of the buildings is in the range of 12–23 mm, which shows that the partially penetrating curtains with 42 m length can effectively control the surface settlement caused by dewatering. This method provides a solution for the comparison and design of groundwater control scenarios for subway foundation pits in deep and high permeable aquifers.