Incineration is widely adopted in municipal solid waste management, which produces large amounts of municipal solid waste incineration (MSWI) fly ash. The harmless treatment of MSWI fly ash requires the appropriate disposal of heavy metals and dioxins that are enriched in fly ash. This review summarizes recently developed harmless disposal methods for MSWI fly ash including solidification/stabilization, thermal treatment, and separation/extraction. In addition, we discuss heavy metal and dioxin fixation, and the removal capacity of fly ash via solidification/stabilization (including cement solidification, chemical stabilization, hydrothermal processes, and mechano-chemical methods), thermal treatment (including sintering, fuel-burning, or electric melting/vitrification), and separation/extraction (including water-washing, chemical reagent leaching, biological leaching, electrodialysis separation, chemical reagent extraction, and nanomaterials extraction). The advantages and disadvantages of different harmless treatment methods are compared and future research prospects and suggestions are summarized. This review provides general guidelines for the harmless treatment of MSWI fly ash in the future.