This letter presents a novel inverse design method for substrate-integrated waveguide (SIW) devices. The internal multiport method (IMPM) is extended to automatically configure the metallic vias, and the EM structure design is solved with binary-option vector numerical optimization methods by simply setting the design objectives. This approach is more efficient than EM simulation and avoids sophisticated structural analysis steps in the design process. Application examples demonstrate the proposed design method and highlight the efficiency of this approach.