Microwave simulation is significant in identifying a reactor design allowing the biomass to be heated and processed evenly. This study integrated the radio frequency and transient heat transfer modules to simulate the microwave distribution and investigated the performance of microwave heating in the cavity. The simulation results were compared with the experimental findings using the finite element analysis software of COMSOL MULTIPHYSICS to predict the temperature profile and electric field of microwave in the biomass (empty fruit bunch pellets). The higher temperature distribution was observed at the bottom and centre section of the empty fruit bunch pellet bed in the reactor, showing the uniqueness of microwave heating. According to the simulation results, the temperature profile obtained through the specific cavity geometry and dielectric properties agreed with the experimental temperature profile. The simulated temperature profile demonstrated a logarithmic increase of 120 °C/min at the first 50 s followed by 50 °C/min until 350 s. The experimental temperature profile showed three different heating rates before reaching 300 °C, including 78.3 °C/min (50–120 °C), 30.6 °C/min (121–250 °C), and 105 °C/min (250–300 °C). The results of this study might contribute to the improvement of microwave heating in biomass torrefaction.