The present work studies numerically the heating of multilayer porous packed bed which is subjected to the microwave radiation with a rectangular waveguide. The multilayer porous packed bed consists of the layers of fine and coarse beds. The simulations of electromagnetic field are described by solving Maxwell’s equations with the finite difference time domain (FDTD) method. The flow fields and the temperature profiles are determined by the solutions of the Brinkman–Forchheimer extended Darcy model, energy, and Maxwell’s equations. The study aims to understand of the influences of layered configuration, layered thickness, and operating frequency on the transport processes in a multilayer porous packed bed. The results show that all parameters have significant effect on the distributions of electromagnetic field inside a waveguide, temperature profiles, and velocity fields within the multilayer porous packed bed.