Integrated TLS and GPR data can provide multisensor and multiscale spatial data for the comprehensive identification and analysis of surficial and subsurface information, but a reliable systematic methodology associated with data integration of TLS and GPR is still scarce. The aim of this research is to develop a methodology for the data integration of TLS and GPR for detailed, three-dimensional (3D) virtual reconstruction. GPR data and high-precision geographical coordinates at the centimeter level were simultaneously gathered using the GPR system and the Global Navigation Satellite System (GNSS) signal receiver. A time synchronization algorithm was proposed to combine each trace of the GPR data with its position information. In view of the improved propagation model of electromagnetic waves, the GPR data were transformed into dense point clouds in the geodetic coordinate system. Finally, the TLS-based and GPR-derived point clouds were merged into a single point cloud dataset using coordinate transformation. In addition, TLS and GPR (250 MHz and 500 MHz antenna) surveys were conducted in the Litang fault to assess the feasibility and overall accuracy of the proposed methodology. The 3D realistic surface and subsurface geometry of the fault scarp were displayed using the integration data of TLS and GPR. A total of 40 common points between the TLS-based and GPR-derived point clouds were implemented to assess the data fusion accuracy. The difference values in the x and y directions were relatively stable within 2 cm, while the difference values in the z direction had an abrupt fluctuation and the maximum values could be up to 5 cm. The standard deviations (STD) of the common points between the TLS-based and GPR-derived point clouds were 0.9 cm, 0.8 cm, and 2.9 cm. Based on the difference values and the STD in the x, y, and z directions, the field experimental results demonstrate that the GPR-derived point clouds exhibit good consistency with the TLS-based point clouds. Furthermore, this study offers a good future prospect for the integration method of TLS and GPR for comprehensive interpretation and analysis of the surficial and subsurface information in many fields, such as archaeology, urban infrastructure detection, geological investigation, and other fields.