Long tunnels through the karst terrain are the challenge area in the railway and highway tunnel construction. To explore solutions for the tunnel through the well-developed karst area, this paper elects a case history of geotechnical investigation, design construction in karst terrain of a segment of the Shenzhen Metro Line No.16 project. Mitigation method was based on the site specific conditions, such as, horizontal and vertical distributions of karst rock cavities and their sizes, karst feature development as well as the characterization of the filling materials, and the compaction grouting method, permeating grouting and the combination of compaction grouting and filling grouting method were selected for the karst mitigation. The satisfactory mitigation results were verified by integrated geophysical methods as well as the coring method.