This invention discloses a method and equipment for producing pure water used in pharmaceutical plant, by using membrane separation and electro-deionization, by using urban running water as raw water. The procedures are: low pressure membrane filtration, absorption by activated-carbon, precision filtration, nanometer filtration and softening and desalination, electro-deionization and deep softening, electro-deionization and deep desalination, functional charged membrane filtration. This invention method can remove, from water, inorganic ions, organic pollutants, bacteria, virus and other microorganisms. Compared with prior art process, this inventive process has advantages of: low cost, high utilization rate of raw water, no need of regeneration process, no consumption of alkali and acid, no environmental pollution, wide available of raw water, high reliability and continuous production of high pureness water.