Abstract: Under the background of neotectonics, the multistage underground flow system has developed due to the different responses of the main stream and tributaries to the crust uplift. The coupling of multistage underground flow systems thoroughly influences the development of karst. On the basis of the development characteristics of the transverse valleys, the study area is divided into the vadose area, shunted area and exorheic area. The controlling-drain action and the topographic index are examined and the coupling features of the multistage underground flow system are analyzed. Based on the coupling of the multistage underground flow systems, the characteristics of deep karst development are verified with the loss of surface water, water bursting and karst development characteristics of tunnels. The vadose area is a regional water system base, in which deep karst developed well, resulting in the large water inflow of tunnels and the drying up of surface water. The shunted area, except the region near the transverse valleys, is characterized by regional water systems. The developed deep karst makes the surface water connect with deep groundwater, causing the relatively large water flow of tunnels and the serious leakage of surface water. The deep karst developed relatively poor in the regions near the transverse valleys which is characterized by local water systems. The exorheic area is a local water system base, in which the deep karst developed poor, and the connection among surface water and deep groundwater is also poor, resulting in the poor loss of surface water under the tunnel construction. This study may broaden the application field of the groundwater flow system theory, and provide a new perspective for the study of karst development theory. It also provides theoretical guidance for hazard assessment and environmental negative effect in deep-buried karst tunnel construction.