Disclosed is a method for clean metallurgy of molybdenum, comprising the steps of: 1) leaching a calcified molybdenum calcine, which is obtained by roasting molybdenite with the addition of calcium, by using an inorganic acid, to obtain an inorganic acid leachate containing molybdenum; 2) extracting same with a cationic extractant to obtain an organic phase loaded with molybdenum acyl cations and a raffinate, 3) using a hydrogen peroxide solution as a stripping agent to obtain a molybdenum stripping solution; and 4) heating the molybdenum stripping solution to dissociate the peroxomolybdic acid therein so as to form a molybdenum acid precipitate, and then subjecting same to calcination to obtain a molybdenum trioxide product. The present method solves the output problem of ammonia nitrogen wastewater, and can also be used for the enrichment and recovery of rhenium.