To evaluate the deformation control effect of the reinforcement scheme for channel under-passing railway bridge during excavation，this paper takes the second channel of the Grand Canal under-passing the Shanghai-Kunming high-speed railway as an example. It carries out a three-dimensional finite element simulation to analyze the displacement deformation of the soil and structures at different stages，including the construction of enclosure structures，channel excavation，concreting of channel structures，and channel navigation. In addition，it conducts the quantitative evaluation on the safety of the enclosure structures and bridge piers during the construction. The results show that the solid support system and layered excavation combined with multiple dewatering can alleviate excessive settlement and bottom heave caused by excavation. The reinforcement scheme also protects the existing structures，ensuring the running safety of trains during the construction.