There is a water culvert with masonry structure in the mountain of Hanguguan Tunnel. Soil deformation caused by tunnel excavation leads to channel cracking. On the one hand, channel water infiltration leads to loess tunnel collapse, which can easily cause engineering accidents and delay the construction period. On the other hand, it will affect the channel water supply and cause social problems. In this paper, the spatial deformation of the tunnel excavation process in the loess layer is revealed through the settlement of the vault in the tunnel, the monitoring of the convergence of the perimeter, and the force monitoring of the lining support structure of the Hanguguan tunnel, and the influence of the tunnel excavation deformation on the culvert is revealed through numerical calculation. The results show that the arch at the tunnel exit has the largest settlement deformation, the larger cumulative settlement, and the faster settlement rate, and the deformation of the culvert is small, only a millimeter. Compared with the monitoring data, the numerical simulation of tunnel excavation and the vertical settlement are basically consistent with the actual situation.