The invention discloses a poly(aryl ether ketone) resin with a main chain containing a polyhedral oligomeric silsesquioxane double-deck structure, and a preparation method thereof, and belongs to the technical field of high molecular material. According to the invention, 3,13-di(2-methoxy-4-propylphenol) octaphenyl polyhedral oligomeric silsesquioxane is taken as a raw material, and is reacted with difluoroketone monomers such as 4,4'-difluoro diphenylmethanone, 1,4-(4-fluoro-benzoyl)-phenyl or 4,4'-(4-fluoro-benzoyl)-1,1'-biphenyl so as to prepare the low-dielectric constant hydrophobic poly(aryl ether ketone) resin with a main chain containing a polyhedral oligomeric silsesquioxane double-deck structure. Compared with conventional poly(aryl ether ketone), the poly(aryl ether ketone) resin with a main chain containing a polyhedral oligomeric silsesquioxane double-deck structure possesses following characteristics because of introduction of polyhedral oligomeric silsesquioxane that water contact angle is increased obviously, and the largest water contact angle can be 100 DEG, dielectric constant is reduced obviously, and the smallest dielectric constant can be 1.95. The synthetic route of the preparation method is simple; and the poly(aryl ether ketone) resin with a main chain containing a polyhedral oligomeric silsesquioxane double-deck structure possesses excellent hydrophobic performance and low dielectric constant, and is a high-molecular material with excellent comprehensive properties and a promising application prospect.