With the improvement of the urban rail transit network, single straight tunnel can no longer meet the demand, and the new tunnel is inevitably close to the buildings, which is bound to endanger the buildings and even cause serious safety problems. Therefore, based on a project in Zhengzhou, the finite element software Midas GTS NX is used to carry out numerical simulation to study the effect of isolation pile protection measures during the construction of small radius shield tunnel, and the accuracy of numerical calculation is verified based on monitoring data. The results show that: 1) Under the absence of shelter pile protection measures, the construction of small radius shield tunnel will cause the lateral settlement deformation of the ground surface, which endangers the operation safety of the railway line; 2) Under the shelter pile protection measures, the impact of the small radius shield tunnel construction on the railway bridge is within the controllable range, which can effectively reduce the deformation of the railway bridge caused by the construction of the shield tunnel and its additional internal force, which is conducive to the operation safety of the railway line; 3) The comparison of monitoring data and numerical calculation shows that the isolation pile protection measures are effective for ensuring the operation safety of the railway line. The results can provide important engineering practical value for the construction of shield tunnels crossing railway bridges safely.