The invention discloses a super-hydrophilic underwater super-hydrophobic separation membrane as well as a preparation method and application thereof. A nano composite material of a super-hydrophilic micro-nano structure is prepared by loading monodispersed hydrophilic nanoparticles on the surfaces of nanoparticles. The nano composite material is dispersed in a mixed aqueous solution of polyacrylamide and methyl cellulose, and after intensive stirring, a membrane formation liquid is prepared. A circular porous support body is infiltrated with water and place on a horizontal surface, a certain volume of the membrane formation liquid is slowly and uniformly dropped and smeared to the surface of the support body, and a super-hydrophilic/underwater super-hydrophobic micro-filtration membrane layer is prepared after drying and sintering.