Extra care should be taken when new tunnels pass through an existing tunnel. If it is not handled properly, this will affect the operation safety of the existing line, and bring security risks to the train’s operation. In order to study the impact of an under-crossing parallel double-line shield tunnel on the existing shield tunnel structure, the influence of tunnel construction on the deformation of overlying strata was analyzed, and the formula for estimating the formation settlement at depth Z below the surface, caused by the excavation of a double-tunnel parallel tunnel, was deduced. Then, a series of three-dimensional finite element numerical simulations were carried out. We analyzed and systematically studied the adverse effects of the tunnel structure of Guangzhou subway Line 5, caused by the tunneling of subway Line 18, evaluated its structure and operational safety, and provided suggestions for site construction. This research demonstrates the following conclusions. (1) The tunnel structures of subway Line 5 and Line 18 are mainly in the strongly weathered argillaceous siltstone stratum, and lightly weathered argillaceous siltstone stratum, respectively, and the stratum where the Line 18 tunnel is located is relatively safe. (2) According to three-dimensional finite element numerical simulation analysis, during the shield-tunneling process of subway Line 18, the maximum X horizontal displacement, the maximum Y horizontal displacement, and the maximum Z vertical displacement of the tunnel structure in subway Line 5 are 1.09, 3.50, and 4.55 mm, respectively. It is considered that the impact of the shield-tunnel penetration of subway Line 18 on the tunnel structure of subway Line 5 is relatively controllable, and does not affect the structure and operational safety. (3) It is suggested that settlement monitoring should be strengthened within the range of 12 m (about 1.5 tunnel diameter D). before and after the excavation axis of the underpass tunnel, and it is necessary to carry out local reinforcement treatment, to prevent adverse effects on the operation of the existing tunnel.