The deformation of surrounding rock is not easy to be controlled in the integral construction of inclined shaft, shaft station, and main tunnel crossing section of water diversion tunnel. Based on the intersection of  Longtan #2 branch tunnel and main tunnel project of Chuxiong section, No. 8 bid of Central Yunnan Water Diversion Project, a numerical model is established by FLAC 3D to simulate the tunnel construction process. The displacement variation law of different regions in the process of tunnel construction is analyzed, the main adverse influence area is found out, and the reasonable construction scheme is put forward and compared with the actual monitoring and measurement. The results show that: (1) The deformation speed is the fastest at the initial stage of tunnel excavation and the deformation of surrounding rock increases with the increase of tunnel crosssection after tunnel excavation. (2) The structural stability of the surrounding rock at the intersection of the main and branch tunnels is poor, and the displacement of the surrounding rock is the largest; The maximum displacement is located at the connection of the main and branch tunnels in the middle of the intersection, and the surrounding rock in the right of main tunnel at the intersection is affected by the construction of the shaft station, leading to the result that the structural stability is weakened, and the left arch waist shows the deformation characteristics of outward expansion. (3) The stability of surrounding rock in intersection area can be effectively improved by using small pilot tunnel construction method, strengthening support, and single direction construction near the intersection.