There is a risk of foundation softening caused by internal water leakage during the operation of hydraulic shield tunnels, which will affect the loading capacity and deformation of lining segments. Based on an engineering hydraulic shield tunnel, a three-dimensional finite element numerical model of tunnel segments, peastone grouting and surrounding rock was built to analyze the variation of bearing performance of lining segments under uniform and non-uniform softened base caused by internal water leakage with class-V surrounding rock. Results show that under the actions of internal and external loads, the circumferential stress, vertical displacement of segments and the stress of assembling pin increase with the increase of the softening depth of the base. The peak tensile stress of the invert segment is 1.88 MPa under uniform softening condition, which increases the risk of segment cracking. The base softening leads to the increase of the peak stresses of the assembling pins, but only has a slight influence on the vertical displacement of the segments. The research can provide a technical basis for the safe operation monitoring of hydraulic shield tunnels.