The organization program of soil investigation which is different from domestic conventional project of marine bridge and tunnel have been adopted in island-tunnel project of HZMB. The geotechnical investigation organization was set up to connect design during investigation. Domestic and foreign design and consulting companies supervised and directed the soil investigation together to make sure that the investigation results were satisfied by designer. International standards were followed, large-scale geotechnical equipments of advanced level were used (such as offshore hydraulic driven jackup, separate hydraulic driven drilling rig, seabed CPTU rig), undisturbed samples have been minimized the disturbance, targeted laboratory tests combining the designing requirements were carried out under international levels, the three-dimensional geological model have been adopted to process geotechnical data. Based on the above fact, the geotechnical results of island-tunnel soil investigation are better than the conventional soil investigation and approved during construction. After the summary of the organization and implementation of refined soil investigation and comparison with conventional investigation, it is recommended that our experiences of refined soil investigation can be used in domestic large-scale project in the future, also it is useful to promote the refined soil investigation to wildly develop in our country.