Geological defects near or beneath built-up area may lead to sudden collapse of ground surface, and cause fatal accidents with losses in human life and property. To understand the features of underground stratum structure and anomalies in mantled karst area, a three dimensional modeling methodology is developed in this paper. Firstly, Timely data is obtained through surface geology investigation and borehole data. Subsequently, Ground Penetrating Radar (GPR) survey is conducted along the survey lines, which has a mixed orthogonal distribution, and a series of two dimensional GPR profiles are obtained. Concurrently, the detailed information of underground stratum structure and anomalies is resolved by the apexes of diffraction hyperbolas and lateral changes in the reflection pattern, including size, geometry and the location. Finally, based on the integrated analysis of slices being parallel or perpendicular to survey lines, a spatial database relative to the geological map is positioned, and the three dimensional model of geological structure is reconstructed. To verify the validity of the method, an application is performed in Nan’an district in Chongqing city. The results indicate the method can provide a simple and relatively effective way for understanding the subsurface geologic condition in practice.