Three-dimensional integrated circuit(3D-IC) was modeled and simulated based on the finite element model. The thermal distribution and the computation complexity for different model were studied. The 3D-IC models were created and the mesh files were generated by Gmsh. The finite element parameters were extracted and the stiffness matrices were obtained using Matlab. The stiffness matrix was represented by the hierarchical matrix(H-matrix). The storage space and computing time in?solving inverse matrix of stiffness matrix were generated for different model. The results show that the computation time and the storage space for solving different complexity of 3D-IC model present linear relationship as the increase of the number of the stiffness matrix ranks.