Civil 3D，as a BIM design and application solution for the geotechnical investigation industry，has become one of the 3D geological modeling implementation technologies. Considering the different engineering geological characteristics of the overburden layer in port and waterway engineering prospecting area，the construction idea of “point-plane-volume”3D geological modeling is adopted，and the modeling methods of the single and complex overburden layer geological models are respectively proposed. Combined with a ship lock engineering case，through the overburden boundary line introduction，curved surface segmentation，curved surface enclosure，and other technologies，the 3D geological model of the site surface rock and soil is refined expressed，and the geological development and distribution of the overburden in the survey area are accurately and intuitively displayed. The research results have great practical significance for the subsequent geotechnical investigation BIM application，such as earthwork calculation，foundation pit excavation design，and so on.