Integral immersed pipe construction is commonly used in Long distance water diversion in the city. The drainage process in the operation phase will cause changes in the stress and deformation of the pipeline structure, which will have potential risk to maintenance personnel and the pipelines. In the background of the Yongjiang Water Diversion Project in Nanning City, the changes in the force and deformation of the pipeline during the drainage process have been studied. The result indicates that the pipe would not be floated until the water level was lower than the top of the pipe. The shell of pipe is under pressure by water, and the stress is increased on the shell of pipe with the water-pressure reduced obviously. The stress of the pipeline is satiated to design requirements in the drainage process.