Abstract: The behavior of land subsidence was obviously affected by layered settlement. It is proved by analyzing the settlement effect because of well pumping test before excavating Yi Shan Road station of Shanghai Rail Transit Line 9.The repeated change between elastic water yield and storage of the seventh confined aquifer is affecting soil layer settlement-heave movement, and the trend falls down. The nearest distance between Rail Transit Line 3 and the subway foundation pit is only 11m, when dewatering on a large scale, the environment effect can be improved in deep foundation pit dewatering by controlling layered settlement effectively through having an appropriate collocation of pumping wells, deepening diaphragm to 62m, reinforcing moisture layer and so on.