The invention provides a clean utilization method for municipal sludge. According to the method, the municipal sludge is subjected to high-temperature anaerobic fermentation, then, a thiobacillus thiooxidans enriched bacterial solution is added for culture, and finally, the municipal sludge is dehydrated. By the clean utilization method for the municipal sludge, provided by the invention, biogas can be produced and prepared at an anaerobic digestion stage; after heavy metals are removed through thiobacillus thiooxidans treatment, the sludge can be fully decomposed; meanwhile, for municipal industrial sludge, in the case that the content of the heavy metals is in the range of exceeding the heavy-metal limit value, specified by the national sgricultural standard, by five times, the heavy metal removal effect is good, the removal ratio can reach 90-95%, the treated industrial sludge can fully meet the agricultural requirements of sludge, is made into all types of organic fertilizers, is applied to landscaping, agricultural use and the like and is used for increasing the content of organic matters in soil and improving the structure of the soil; whereas, for municipal domestic sludge, the heavy metal removal effect is more obvious.