A set of coupled integral equations is presented based on Love’s and Schelkunoff’s field equivalence principles. According to Love’s equivalence principle and the boundary conditions, a general form of the Poggio–Miller–Chang–Harrington–Wu formulation is applied for modeling the waveguide cavities containing composite structures. The structures are discretized using the higher order polynomial basis functions, whose orders are adaptively adjusted for accurately modeling current distributions in this kind of strong near-field coupling and resonance problems. Moreover, the integral equations for the apertures involving the waveguide ports, each of which is terminated by a semi-infinite waveguide, are established according to Schelkunoff’s equivalence principle and the boundary conditions. Because the free-space Green’s function as well as the spatial discretization-based basis functions cannot be applied to semi-infinite waveguides, we employ waveguide eigenfunctions as the basis functions for the outer surface of an aperture. These coupled integral equations are then solved numerically using the method of moments accelerated by the parallel computing techniques. Comparisons with two well-developed software products demonstrate the accuracy and efficiency of the proposed method.