Due to the limited geological data and the complex stratigraphic relationship in actual project, the accuracy of traditional geological modeling methods could not meet the engineering requirements in precision. Potential field theory integrates contact data and direction data of stratum interface and interpolates gradient field by co-Kriging method, which makes the geological model more accurate and more in line with the actual stratum structure. Based on the potential field theory, and taking borehole data of a section of Nanjing Metro Line 5 as the main data source, this paper established a refined three-dimensional geological model through some steps of model size analysis, stratum merging, soil contact analysis, and etc. A refined analysis is also conducted on the spatial distribution characteristics of compression modulus of the key soil layer③-1b1-2 crossed by metro line. The results show that there are obvious advantages existed in the three-dimensional geological modeling method based on potential field theoryfor the modeling of complex geological conditions. The refined analysis of the spatial distribution of key soil parameters is of great significance for guiding engineering design and construction.