In this manuscript, a methodology for three-dimensional geological modeling and visualization in dredging engineering was proposed to understand and analyze the spatial distribution of soil conditions in complex underwater geological settings for dredging engineering comprehensive and enhance the operational efficiency of dredgers. A three-dimensional digitized platform for dredging engineering was established by using computer technology, database management, visualization techniques and 3D geological modeling. The intelligent system of dredging engineering geological database is mainly developed using the .NET as the program development platform and C# and C++ as language. This system realizes the functions of engineering geological data storage and management, 3D geological modeling, dredging engineering analysis, and so on. The practical application showed that the system boasts not only fast 3D modeling speed, strong operability and high conformity with the actual geological situation, but also the dredging engineering analysis module, which greatly improves the quality and efficiency of construction. It can meet the actual needs of dredging engineering well and has broad promotion and application prospects.