The migration, transformation and ecological risk of heavy metals (Cr, As, Ni, Cu, Zn, Cd and Pb) in the sewage sludge during the microwave-assisted thermal hydrolysis process were investigated under different temperatures (80 °C, 100 °C, 120 °C, 140 °C, and 160 °C). The potential relationship between the bio-availability of heavy metals and the variables of microwave treatment, including pH, ammonium-nitrogen, soluble chemical oxygen demand, pH, soluble protein, soluble polysaccharide and volatile solid, was also explored. The results showed that the migration of heavy metals between solid-liquid phase mainly depended on the temperature. The percentage of all heavy metals (except Cu) in mobile (acid-soluble/exchangeable and reducible) forms decreased after microwave-assisted thermal hydrolysis treatment. The solubilization of compounds with C = O and O-H accompanied with the generation of organic and inorganic metal halides were also observed in the treated sludge through fourier transform infrared spectroscopy analysis. NH4+-N showed the highest negative correlation to the bio-availability of most heavy metals (except Cu and Cr) with coefficients (absolute value) over 0.87 (P < 0.05). VS showed a positive correlation to the bio-availability of most heavy metals (except Cu). The total potential ecological risk index (RI) decreased by 46.65% after microwave treatment at 160 °C.