With the rapid development of transportation construction, the density of highway, railroad and subway tunnels crossing the same mountain range is getting higher and higher. The construction of new tunnels will destroy the seepage balance of the existing tunnels in the tunnel site area, affect the water inflow and pore water pressure of the first-built tunnels, and cause changes in the stresses of the tunnel surrounding rocks and even affect the operation safety of the existing tunnels. Taking Chongqing Tongluo Mountain Range (called Nanshan in Nanan District, Chongqing) as the background, the three-dimensional finite element analysis of the construction process of new tunnels is used to study the impacts of the construction of new tunnels between the Nanshan Tunnel and the Tongluo Mountain Tunnel on the drainage of the existing tunnels, as well as the seepage characteristics of the new tunnels and the prediction of the influx of water under the conditions of the existing tunnels. This study provides a reference for analyzing the evolution of the groundwater system caused by the construction of multiple tunnels in the karst valley area and predicting the amount of water inflow from the new tunnels.