The invention provides a system for preparing magnesium hydroxide from desulfurized waste water. The system comprises a first reaction tank which is used for separating calcium ions and a second reaction tank which is used for separating magnesium ions, wherein a water inlet of the first reaction tank is connected with a desulfurization tower through a preprocessing unit; a water outlet of the first reaction tank communicates with a first pipe type membrane device; a water inlet of the second reaction tank communicates with a liquid outlet of the first pipe type membrane device; and a water outlet of the second reaction tank communicates with a magnesium hydroxide purifying unit. According to the system disclosed by the invention, in the course of softening the desulfurized waste water, the purity of the magnesium hydroxide is improved, so that the magnesium hydroxide meets the application standard or the sale standard, and economic benefits are generated; and when waste water is treated, waste is changed into wealth, so that the system conforms to the ideas of energy conservation and emission reduction.