Municipal solid waste circulating fluidized bed incineration (MSWCFBI) fly ash was a hazardous waste, maintaining challenges for disposal. One effective approach was stabilizing the toxic heavy metal ions in the fly ash structures in situ. This work proposed a fusion-hydrothermal method, including fusion pretreatment in nitrogen atmosphere and microwave-assisted hydrothermal process, to treat three MSWCFBI fly ash samples. Specifically, leaching tests were performed to demonstrate the heavy metal stabilization. Through the treatment of the fusion-hydrothermal process, the concentrations of Cd, Cu, Zn, Pb, Ni, and Cr ions leaching from the fly ashes were obviously less than those of the raw fly ash and the sample only treated by hydrothermal process. Meanwhile, the heavy metal ions migrating from the fly ash to the hydrothermal residual liquid were reduced. Importantly, lots of zeolites formed during the fusion-hydrothermal process, such as to bermorite and sodalite. The fusion pretreatment significantly facilitated the conversion of quartz into amorphous silicon and silicate salts. Then, the silicon dissolution was accelerated and zeolite formation was promoted. Eventually, the heavy metal ions could be trapped in zeolite frameworks, enhancing the stabilization of heavy metal. Moreover, the cation-exchange capability values of the three treated fly ash were 1.099, 1.168, and 1.188 meq g −1 , two-folder larger than those of the samples only treated by hydrothermal process. In summary, the fusion-hydrothermal method could facilitate the stabilization of heavy metal ions in the fly ash and the as-obtained solid product with high content of zeolite was promising for future applications.