Adopted advanced physical and mechanical prospecting, in-situ testing and other new surveying technologies, the spatial distribution and physical ad mechanical properties of four weathered deep troughs developed from basic rocks are detected in the sea area where the tunnel runs through. A set of advanced and effective onshore drilling and hydrological test technologies was employed while multiple subsea tunnel water quantity analysis model was applied to measure the water quantity in the tunnel and weathered deep trough permeability and stability of subsea tunnel, which findings are leading in China. The most advanced “3D geosphere information system” was employed to supervise 3D geosphere model, playing a significant role in tunnel position optimization design. Comprehensive surveying mode for subsea tunnel is established with greater breakthrough and innovation in technology.