A new methodology has been developed, based on moment method; for analyzing a class of rectangular waveguide based circuits and radiators. The methodology involves in modeling the given structure using tetragonal bricks or cavities and then replacing all the apertures and discontinuities with equivalent magnetic current densities so that the given structure can be analyzed using only the Magnetic Field Integral Equation (MFIE). As it is necessary to use a number of such cavities in order to study these complicated waveguide structures, the present method is named as Multiple Cavity Modeling Technique (MCMT). The major advantage for using the MCMT in rectangular waveguide based structures is the fact that since only the magnetic currents present in the apertures are considered the methodology involves only solving simple magnetic field integral equations rather the coupled integral equation involving both the electric and magnetic currents. Further it is possible to consider both co and cross polarization and also the thickness of the waveguide discontinuities like diaphragm thickness or window thickness in the analysis. Due to this, it is possible to get highly accurate result. It is also possible to extend the method to any number of resonators, cavities or irises regardless of the polarization. To demonstrate, the methodology has been applied to analyze an open end of a waveguide with dielectric plug, both in transmitting and receiving mode, and a waveguide step discontinuity. Even mode and odd mode admittances of interacting identical inductive diaphragms have also been calculated using this methodology. Data obtained using this technique has been compared with measured, CST microwave studio simulation and literature available data. The theory has been validated by the reasonable agreement obtained between experimental data, simulated data and literature available data with numerical data.