The invention provides a synergistic harmless treatment method for electrolytic manganese residues and phosphogypsum. The synergistic harmless treatment method for electrolytic manganese residues andphosphogypsum comprises following steps: (1), the electrolytic manganese residues and phosphogypsum are uniformly mixed in a dry basis mass ratio of the electrolytic manganese residues to phosphogypsum of 1:(2-5); (2), slurry is prepared from a mixture obtained in step (1) in a solid-liquid mass ratio of 1:(0.3-0.7), pH of the slurry is regulated by adopting an alkaline agent prepared from one ormore of 1-2 parts by weight of a burning raw material, 2-3 parts by weight of calcium oxide and 1-3 parts by weight of magnesium oxide, and pH value of the slurry is kept in a range of 6-9; (3), a mixed material obtained in step (2) is conveyed into a stockpiling place for stockpiling or other use. Compared with the prior art, soluble fluorine, phosphorus, manganese and ammonia nitrogen in the phosphogypsum and the electrolytic manganese residues can be effectively immobilized, and meanwhile, the method further has the advantages that reaction conditions are mild, the technological process issimple and easy to operate, treatment cost is lower and the like.