In order to explore the impact of settlement caused by pumping on subway system, three dimensional seepagestress coupled numerical simulation method is used to simulate the settlement caused by confined water exploitation and to study its influence on the station-tunnel system in the soft soil area in Binhai district of Tianjin. Under certain assumptions, the settlement between different parts of metro station-tunnel system and the stress concentration caused are quantitatively analyzed. The results show that: (1) Compression and settlement in confined water layer is the largest, and compression decreases upwards and downwards; (2) When settlement occurs, station structure has certain resistance, while tunnel structure′s resistance is weaker, which causes differential settlement in tunnel near station and large stress concentration at the top of tunnel about 2 m near the station.