The extra deep circular shaft excavation of Yunling and Miaopu comprehensive facility of the drainage and regulation project in the Suzhou River section requires to control the water level of the third confined aquifer in Shanghai for the first time. Based on the analysis of the distribution characteristics of the confined aquifer and the dewatering measures taken by Yunling comprehensive ficility, the control technology and effects of deep confined water in soft soil area are analyzed based on the measured data. The results show that the two-layer water isolation measures of shaft ground wall and outer cut-off wall adopted by the project accomplished the dewatering of the third layer confined water in Shanghai region for the first time, and the maximum water level drop reached 57.8 m, which ensured the stability of the foundation pit. The measured data show that the water level drop outside the cut-off wall was smaller than that between the cut-off wall and the retaining structure, so was the water level drop rate. The change of pore water pressure in each soil layer corresponded to the dewatering of the confined water. After the restoration of the confined water level, the deep pore water pressure on the soil facing surface increased significantly, and the deeper the depth, the more obvious the increasing trend of the pore water pressure; however, the change of water pressure on the pit facing surface was relatively gentle. The conclusions can provide some reference for the construction of similar projects and the development of deep underground space in Shanghai region in the future.