Due to the influence of grouting technology and formation property, the segment of shield tunnel is easy to have defects such as cavity behind the wall. In order to investigate the deformation response mechanism of shield tunnel segments with a cavity behind the wall, a three-dimensional refined numerical model of shield tunnel considering the ring and longitudinal joints was established, the ovality after loading, joint opening and dislocation of the hollow segment structure under the action of different stratum properties, tunnel buried depth, back clearance, elastic modulus of grouting ring and initial ellipse of segment were analyzed. The results show that the structural deformation will be aggravated by the decrease of stratum self-stability, the increase of tunnel buried depth, the increase of back-wall clearance and the decrease of stiffness after slurry solidification, under the condition of the same deflection angle, the larger the initial ellipse is, the smaller the deformation is, and the critical depth of the tunnel is about 0.5 ~ 1.0 m when the tunnel depth is 10.8 m. The influence of the tunnel waist cavity on the structural deformation is listed as follows: segment dislocation < ellipticity < joint opening after loading.