The present article investigates the trunk canal of South-to-North Water Transfer Project constructed beneath the "Yu-ji" railway tunnel and crossing it. The three-dimensional numerical simulation FLAC3D is carried out to simulate the construction process,the results show that the canal structure is relatively stable when the distance between the top of the tunnel and the bottom of the trunk is about 32.24m. Besides the displacement becomes small when the ground loss rate is controlled at 0.5% or the overburden thickness is more than twice the diameters. It was also demonstrated that the displacement increases with the increase of ground loss rate,while it decreases along with the increase of soil thickness. The results of numerical simulation are compared with the empirical formula,and the results show that they are of high agreement.