The objective of this study was to check the feasibility to treat medical waste incinerator (MWI) fly ash directly through microwave irradiation. The destruction efficiency of dioxins in MWI fly ash and in its froth products after flotation was compared in the air/nitrogen (N2) atmosphere. Results demonstrated that the dioxin destruction effect was better in a N2 atmosphere than that in an air atmosphere. And the total dioxin mass destruction efficiency of fly ash and the froths were 55.4% and 95.6% in the air atmosphere, while their values were 65.0% and 98.4% in the N2 atmosphere, respectively. The vaporisation ratio of dioxins in MWI fly ash was up to 10.2% after 9 min N2 irradiation. Furthermore, dechlorinating reactions of dioxins would occur when MWI fly ash was treated in N2 atmosphere. Therefore, microwave-absorbing additives should be used to improve the decomposition of dioxins because of MWI fly ash containing less carbon constituents than the froths.