Abstract: The development and utilization of urban underground space is an important part of urban construction, and urban three-dimensional geological model is one of the bases to evaluate the difficulty of development and utilization of underground space. In order to meet the needs of current urban construction, this paper designs a reasonable calculation method of stratigraphic pinchout position based on the influencing factors of model accuracy. This method determines the pinchout position when tracking stratigraphic division by considering factors such as stratum thickness, borehole spacing, stratum burial depth, and single-hole control range, so as to construct a stratum surface with higher accuracy, and solve the problem of inaccurate stratigraphic division range in 3D geological modeling. In this paper, Beihai City is taken as the research area to establish a unified stratigraphic sequence, generate stratigraphic zoning constraints, and establish a three-dimensional geological structure model of Beihai City by using drilling and profile data. In order to verify the reliability of the constructed model, this paper evaluates the model quality based on drilling and profile. The results show that the three-dimensional geological model constructed by this method is highly consistent with the actual situation, which can deal with the modeling problem of unconformity strata containing complex strata and has certain credibility.