This paper presents an experimental study on the applicability of microbial induced carbonate precipitation (MICP) to treat municipal solid waste incineration (MSWI) fly ash with high alkalinity and heavy metal toxicity. The experiments were carried out on fly ashes A and B produced from incineration processes of mechanical grate furnace and circulating fluidized bed, respectively. The results showed that both types of fly ashes contained high CaO content, which could supply sufficient endogenous Ca for MICP treatment. Moreover, S. pasteurii can survive from high alkalinity and heavy metal toxicity of fly ash solution. Further, the unconfined compressive strength (UCS) of MICP treated fly ashes A and B reached 0.385MPa and 0.709 MPa, respectively. The MICP treatment also resulted in a reduction in the leaching toxicity of heavy metals, especially for Cu, Pb and Hg. MICP had a higher solidification and stabilization effect on fly ash B, which has finer particle size and higher Ca content. These findings shone a light on the possibility of using MICP technique as a suitable and efficient tool to treat the MSWI fly ash.