Municipal sludge contains high amounts of proteins as well as a variety of heavy metals which limits the utilization of sludge proteins as a resource. In this paper, humic acid had been used to decrease the heavy metals in protein that was extracted from sewage sludge. Based on the influence of humic acid on the properties of sludge and the form of heavy metals in sludge, the effect and mechanism of humic acid on the characteristics of proteins were discussed. The results demonstrated that pretreating sludge once with 0.1% humic acid not only decreased the amount of heavy metals, but also decreased their mobility and bioavailability, increasing the removal efficiency of Cr, Cu and Zn by 23.7%, 35.5% and 13.4%, respectively, from the extracted protein. Additionally, no As, Cd, Mn, Ni, or Pb had not been detected. During this process, humic acid also had an effect on the secondary structure of proteins, which was primarily seen in α-helix and β-sheet. In particular, the hydrogen bonding between the structures was disrupted, causing the regular structure to unfold and gradually change into deformed and random coils, while the relaxed and parallel structures with relatively poor stability progressively converted into more stable forms.