Shaking flask experiments were used to study the indigenous microorganisms leaching of heavy metals from sediment in the optimum conditions,which were determined to be pH =3.0,65℃ and 7% pulp density.Residues from the bioleaching were analyzed through XRD and three-stage BCR sequential extraction procedure.Results show that heavy metal(Cd,Mn,Cu,Pb,Zn) contents sharply decrease over 7 days leaching,from 4 530 mg/kg,7 650 mg/kg,830 mg/kg,29 530 mg/kg,62350 mg/kg to 730 mg/kg,1280 mg/kg,390 mg/kg,13 810 mg/kg,15650 mg/kg respectively.Acid extractable percent content decreases remarkably during the bioleaching process;meanwhile,residual form percent content rises obviously.The environmental availability and potential risk of heavy metals are less than the standards listed in Hazardous Waste Distinguishable Standard (GB 5085.3-2007).Indigenous microorganisms can efficiently implement the resources and harmlessness of heavy metals in sediment.