Abstract The excavation by earth pressure balance (EPB) shield could cause stress fields varied, which is harmful to adjacent existing structures. Thus the effect of excavation clearance of the EPB shield on the settlement of existing structures should be taken into account. The transit tunnel from Meicun to Shangmeilin of Shenzhen Metro Line 9 constructed by the EPB shield with mid-shield-grouting was investigated. The deformation of existing tunnel is analysed by three-dimensional (3D) finite element methods (FEM). It is found that the settlement of overburden soil is obviously influenced by the structure of the existing tunnels through the plastic development of the soil. The rate of settlement is remarkable when the shield effect zone approaches the existing tunnels so that timely mid-shield grouting is an efficient method of controlling the settlement induced by the excavation clearance. However, the grout used in this method should be with the properties of short hardening time, large elastic modulus and low shear strength. Different standards of settlement control should be employed with respect to different underground tunnels, in which minimum elastic modulus of the filler that is usually determined by fitting function. This can be taken as a guide rule of the selection of material parameters in the project. The simulation results are in good agreement with the settlements measured for the existing tunnels and the ground surface. The parameter sensitivity analysis by means of the Spearman’s correlation coefficients shows that the elastic modulus of filling material significantly influences on the settlement of the existing tunnels and the ground surface.