The invention discloses an electrolytic manganese electrolyte salt residue salt separation method and system, and belongs to the field of wastewater treatment, and the system comprises a dissolving tank, a filter press, a primary buffer tank, a primary cooling crystallization system, a first centrifugal machine, a secondary vacuum crystallization system, a second centrifugal machine, a secondary buffer tank, a tertiary high temperature crystallization system, a filter press kettle and a concentrated discharge drying system. No agent is added, inorganic components of the electrolytic manganese residues are extracted according to basic physical properties of solid waste and physical separation, and the operation cost is low; inorganic salt is separated in a mother liquor circulation mode, the waste liquor discharge amount is small, and meanwhile a large amount of water resources are recycled. According to the method, the multi-component elemental salts (ammonium, magnesium and manganese) in the manganese slag are recovered in sequence instead of single-component salt recovery in the electrolytic manganese waste slag, the recovery rate is high, and the solid waste reduction treatment degree is high; the electrolytic manganese waste residue inorganic salt separation equipment mainly comprises a reactor and an evaporator, and is simple in system, low in equipment investment and easy to industrialize.