To explore the reasons for the deviation of a certain bridge pier, based on the results of in-situ investigation, it can be concluded that the main reasons for the deviation of the pier are that under the vibration coupling effect the characteristics of the weak and fractured zone beneath the pile , softening of the rock layers on the pile side and bottom, drilling on the pile side, and the rock layers on the pile side and bottom can exacerbate the softening，et al. Numerical simulation results indicated that the softening of the rock layers had the greatest influence on the displacement of the pier, followed by the weak and fractured zone beneath the pile, while the effect of drilling on the pile sides was minimal. After identifying the main reason for the large deviation of the pier, a method of pre-grouting reinforcement is put forward for the second large deviation of the pier in the process of pile patching.Numerical simulations demonstrated that pre-grouting reinforcement could reduce the displacement of pier 6# caused by pile repair by 80%. After optimization, the order of rectification and reinforcement of pier 6# is: pre-grouting reinforcement at the bottom of 5#-8# pile, patching pile, increasing pier section to modify pier.