To ensure the smooth construction of shield tunnel when conventional surface grouting reinforcement is difficult to implement, a case study is conducted on the tunnel between Hefei railway station and Yaohai park station of phase 3 of Hefei rail transit line 1 crossing underneath the Hefei railway station with strict deformation controlling standard in the soft soil stratum. The main factors causing the station deformation during shield tunneling are analyzed, the countermeasures for controlling shield exposed length such as shield attitude control and synchronous grouting optimization are put forward, and a finite element simulation model is established to analyze the influence of shield tunnel underpass construction on the station under different working conditions. Research results indicate the following: (1) The overbreak of the cutterhead and the exposed length of the shield tail are the factors causing the ground deformation during shield tunneling, which should be controlled to minimize the ground deformation around the tunnel. (2) The optimized construction scheme can minimize the influence of the tunnel undercrossing construction on Hefei railway station. (3) It is suggested to conduct intunnel grouting and shield tail synchronous grouting to reduce the construction risk. At the same time, the shield attitude should be controlled to reduce the cutterhead overbreak.