The trial production of marine natural gas hydrates (NGH) in China is gradually increasing, attracting concerns on related environmental issues. The entire regional conditions of engineering geological environment must be investigated thoroughly before NGH production. These conditions should be defined, among others, in terms of seabed topography, stratigraphic structure, soil types, physical and mechanical characteristics, hazardous geological factors and distributions, and hydrodynamic characteristics, which provide a variety of geological spatial information and can be obtained from different sources. Due to the high cost and low efficiency of deep-sea engineering geological drilling, only few stations can be deployed. Hence, not enough data are available for the construction three-dimensional (3D) geological models. This study considered the data of only a few drilling stations and compared them with well logging and 3D seismic data. First, the engineering geological standard strata were established. Second, we interpreted and exported the stratigraphic (based on virtual boreholes) and spatial information (in terms of X, Y, and Z) of existent geological structures in GeoFrame. Finally, using several technical modules of ArcGIS (i.e., ArcMap, ArcScene, ArcCatalog), we constructed a spatial database and a comprehensively intuitive 3D visualization data management platform for engineering geological environmental surveys and evaluations in the hydrate area. By clicking any element included in the platform, the correspondent data or results can be looked over: this efficient and continuous systematic database can be used to support the future production of NGH in the area.