With the improvement of the planning level of underground space, the location of the planned under-crossing tunnel can be known in advance when constructing the upper-span tunnel. Therefore, pre-protection measures can be taken in advance during the construction of the upper-span tunnel. A new pre-protection method of a pipe-jacking channel was proposed to reduce the adverse effects of under-crossing shield tunnels. Numerical simulations of different pre-protection schemes were carried out using the finite element method to analyze its deformation control effect. The simulation results show that the deformation control effect of the gantry reinforcement scheme is the most significant. It is shown that the displacement of the pipe-jacking channel is more significantly suppressed with pre-protection measures than without preventive protection measures. The vertical displacement curve of the pipe-jacking channel exhibits a “W” shape after the construction of the double-lane shield underpass. By comparing the three different working conditions, it is found that the maximum vertical displacement and surface settlement of the pipe-jacking channel greatly reduced the gantry reinforcement pre-protection. Compared with Case 3, the effect of the pre-protection measures adopted in Case 2 was less obvious, which indicated that the form of the pre-protection had an important influence on controlling the deformation of the pipe-jacking channel.