In recent years, many researchers have devoted themselves to the employment of microwave heating for immobilizing municipal solid waste incineration (MSWI) fly ash; however, they only focused on the leaching properties of heavy metals in treated fly ash. Herein, the aim of this study is to systematically investigate the effects of microwave-assisted thermal treatment on the fate of selected elements with conventional thermal treatment as control. The results showed that leaching behaviors of Pb, Cu, and Zn were successfully suppressed, while the leaching concentration of Cr was increased due to the transformation of Cr(III) to Cr(VI) after thermal treatment. Compared with conventional thermal treatment, microwave heating was more efficient for stabilizing MSWI fly ash. Sequential extraction experiment indicated that water-soluble and exchangeable fractions of Pb significantly declined with enhancement of the residual fraction, which manifested that Pb existed in more stable speciation. With regard to Cr, the reducible form was the main fraction in both treated and raw fly ashes. After thermal treatment, nevertheless, the reducible fraction of Cr ascended and the residual Cr descended. Under all conditions, Pb could be effectively evaporated, and the vaporization of Pb reached 90% at 1100 degrees C. By contrast, less than 20% of Cr was vaporized, while higher temperature and longer retention time suppressed the vaporization of Cr. During thermal treatment, CaO was newly generated according to X-ray diffraction results and it accelerated the oxidation of Cr(III). Particle agglomeration and grain growth were observed via scanning electron microscopy, and these processes conduced to depressing the leaching of heavy metals. This study provided a deep insight into the effect of microwave heating on the fate of Pb and Cr in MSWI fly ash.