Karst formations in Southwest China are significantly developed. With the increase in tunnel construction year by year, constructing tunnels in areas of karst geology is inevitable. There are great safety risks associated with exposed karst caves, and the water inside the caves can seriously impact the tunnel structure and its filling materials. Traditional cave disposal technology mainly focuses on safe crossing treatment at the construction stage; however, problems such as backfill collapse and floor floating caused by karst water erosion during the service period are not considered. Therefore, proposals for a new construction scheme to ensure the stability and safety of the tunnel during the service period are urgently needed. Using Huangchongyan Tunnel as an example, we propose a safe crossing scheme of ‘plate–pile–bedrock’ for karst caves, based on a comparison of karst cave treatment schemes at home and abroad. In addition, considering the impact of karst water on the tunnel, we developed a ‘bottom to top’ reverse drainage structure, which solved the problem of floating during tunnel service. In our study, we developed a full life cycle disposal scheme to enable safe passage through tunnels in karst caves, providing a reference for the design and construction of similar projects.