With the development of science and technology and the development of our society, new technologies are continuously applied in our country’s engineering. Due to the complex geological phenomena such as faults, pinching, and outcrops in geological bodies, in order to express these phenomena when modeling 3D strata Regardless of whether it is a surface model, a volume model or a mixed model, there are problems of space division or surface intersecting. Due to the complexity of geological body topology, data errors and computer accuracy problems, these models often fail in the actual modeling process. Using level set theory can effectively solve this problem. Level sets use implicit functions to express surfaces, which can realize the expression of complex geological bodies and topological operations such as merge, intersection, and difference. In 3D geological modeling, after generating various geological interfaces by interpolation, these geological interfaces are expressed in level sets, and various complex topological operations are completed by level theory, and a 3D geological model expressed in level sets is established. On this basis, by inserting various engineering activity interfaces expressed by level set, and using level set theory to perform topological operations, geological models after various engineering activities can be constructed. Reuse algorithms to extract various geological interfaces or engineering activity interfaces, and construct stratigraphic models that can be used for real-time visualization or engineering evaluation (such as finite element calculation) or geological models after engineering activities. By establishing a three-dimensional geological model of the area where the construction project is located, architectural designers and construction personnel can analyze and study complex geological conditions, and provide technical support for engineering. By studying the three-dimensional geological model, this paper analyzes the engineering geological conditions and potential risks of the construction process in the study area, and proposes risk control measures, which can provide scientific decision-making basis for building design, construction, and risk prevention and control, and has a high promotion value. Experimental research results show that the application of computer three-dimensional modeling in engineering engineering can effectively reduce the cost of the project, ensure the quality and schedule, and greatly improve the construction efficiency of the project.