A new method of depostition of organic silicon film by magnetic-controlling plasma polymerization was used to protect Y-Ba-Cu-O superconductor from corrosion.The deposition rate of plasma polymer film with magnetic-controlling is 20 times over that without magnetic-controlling. The relation between the deposition rate of film and th process factors of magnetic-controlling plasma were studied. The Y-Ba-Cu-O superconductor covered with organic silicon film was formed by magnetic-controlling plasma polymerization had been protected from corrosion in water over 48 hours.