An efficient method is proposed to perform the steady-state thermal analysis of multilayer boards by using the multilayer finite-difference method to obtain and solve the thermal conductance network. The electro-thermal analysis of substrate-integrated waveguide SIW filter is further carried out, with its distributed heat source, that is, electromagnetic losses. Then, our method is applied to optimize the electro-thermal performance of a composite configuration, including a SIW filter with a selfheating chip attached on it. A location with the minimum hotspot temperature is found. Good agreement is achieved between the results simulated with our method and the commercial finite element method FEM simulators. When the worst-case error is set to 5.3%, the run time of our method is significantly reduced by 95% in comparison with the FEM simulators. © 2014 Wiley Periodicals, Inc. Int J RF and Microwave CAE 24:594-604, 2014.