The invention provides a system for preparing high-purity magnesium hydroxide based on magnesium-reduction desulphurization waste water. Through the course of aerating, electric flocculation, deoiling, ammoniacal nitrogen removal, COD removal and the like at the pretreatment stage, the desulphurization waste water is pretreated; at the medicine adding and salt separating stage, in the manner of adding double alkali, most calcium ions and a part of magnesium ions are separated out, and then according to a nanofiltratoin technique, univalent ions and divalent ions are separated, so that a solution being high in magnesium ion concentration is obtained; at the magnesium recovery stage, by adding sodium hydroxide, magnesium hydroxide precipitate is obtained, then the precipitate is subjected totreatment of filtration, drying, dehydration and the like, high-purity magnesium hydroxide products are obtained, and through determination, the purity is 99.83%. The system disclosed by the invention is short in technological process, economical and environmentally friendly, and resource reuse is realized in the course of desulphurization waste water treatment.