In this study, experimental investigations were conducted to simultaneous desulfurization and denitrification from stimulated flue gas by the novel microwave reactor with potassium permanganate and zeolite. The study evaluates the influence of microwave power, empty bed residence time (EBRT), inlet concentration, microwave and catalyst on the performance of the microwave reaction system, and the mechanism for microwave induced catalytic SO2 and NOx oxidation was elicited. An understanding of the role of microwave and catalyst on simultaneous desulfurization and denitrification can help evaluate the potential of applying this novel method as an effective SO2 and NOx emission control strategy for the flue gas cleaning.