Nowadays, the protection of existing municipal tunnels is often faced in the construction of urban rail transit engineering, and the influences and protection of existing municipal tunnels should be fully considered in the design and construction stage. Nanjing Metro Line 5 station is near the model road tunnel, and the section shield tunnel passes through the tunnel in a close orthogonal distance. In this paper, the deep foundation pit excavation and section shield tunneling construction of the project are introduced, and such tunnel protection measures are proposed as foundation pit supporting system, shield propulsion parameters and synchronous grouting through numerical simulation and analysis of deformation rules. The supporting axial force, foundation pit and tunnel displacement are tracked and controlled during construction excavation, and the earth pressure, shield thrust and velocity, and tunnel displacement are tracked and controlled during underpenetration period. The results show that the above measures can effectively control the deformation of existing municipal tunnels and ensure the normal operation of model road tunnels during station excavation and shield underpenetration. The content of this paper can provide references for similar rail transit projects.