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.