For the integration of GIS spatial information and a variety of field data obtained by numerical simulation, FEM (finite element method) is necessary to be combined with GIS. To improve the efficiency of system development, the open source softwares, such as GRASS GIS and VTK, are used to establish complex system development framework combining FE simulation and GIS by Python language. The platform named 3DPyGisTFEM enables seamless coupling between FE calculation and 3DGIS for tunneling analysis. Moreover, the algorithm of tunnel model generation connects a series of contour lines with tunnel center lines. The geological sections of tunnel excavation can be obtained by cutting operation on different strata layer DEMs and tunnel models. The triangular meshes for finite element simulation introduced by Delaunay mesh generation algorithm improve TIN model of GIS. The field data of research area are generated by interpolation of multiple geological sections simulation results from FEM. Then, the seamless coupling method with FEM in GIS is realized through comprehensive analysis of field data using GIS spatial analysis methods. The Huangjiazhai tunnel engineering example shows that the ground surface elevation from tunnel crown has greater influence on surface settlement than other factors, such as relative slope, buffer and etc.