Tunnel excavation breaks the original hydrological dynamic equilibrium in the tunnel site area, and promotes the alternation of water cycle; the groundwater system has been recovered to some extent during tunnel operation, but the extent of the recovery and the revelation on the prediction of water influx of the new tunnels in the tunnel site area still need to be studied in depth. Taking the operation tunnel of Chongqing Nanshan (NS) in the karst valley area as an example, based on the analysis of tunnel engineering geological conditions and hydrogeological conditions, the water influx of Nanshan Tunnel is predicted through the monitoring of water outflow from the mouth of the tunnel after the tunnel has been passed through, the measurement of the water influx in the tunnel operation period, and the numerical simulation analysis of tunnel inflow, and at the same time the water influx of the nearby operation tunnel of the Tongluo Mountain (TLS) Railway Transportation Tunnel is analyzed. The results show that the water influx in the right hole of NS Tunnel is more influenced by surface water, while the left hole is more influenced by groundwater and karst water. Rainfall and permeability coefficient of surrounding rock have great influence on the water influx of tunnel. It provides a reference for the study of the evolution law of groundwater system of multiple tunnel construction in karst trough valley area.