Thermal issue is a leading design constraint for three-dimensional integrated circuits (3D-ICs) and through silicon vias (TSVs) are used to reduce the temperature of 3D-ICs effectively. In this paper, the finite difference method-based heat conduction equations is proposed for the thermal analysis of the TSV structures in 3D-ICs and generalized minimum residual method (GMRES) with symmetric successive over-relaxation (SSOR) preconditioning is utilized to solve the resulting temperature matrix equations. Simulation results show the accuracy and efficiency of the proposed method.