The invention discloses a porous nano silicon ion separation film and a preparation method thereof. The porous nano silicon ion separation film is a porous film with nano silicon as a basic skeleton and being of a batt-shaped microstructure, and permanent holes with the average diameter ranging from 1-1000 nanometers are arranged on the surface of and in the porous nano silicon ion separation film. A plurality of hydrophilic active groups such as silicon-oxygen bonds and silicon hydrogen bonds are arranged on the surface of the nano silicon basic skeleton. The preparation method of the porous nano silicon ion separation film is simple, easy to operate and capable of directly separating hydrophilic ions with the radius smaller than 200 picometres and hydrophilic molecules with the radius smaller than 200 picometres from solution and simultaneously discharging hydrophilic ions with the radius larger than 200 picometres, hydrophilic molecules with the radius larger than 200 picometres and all hydrophobic molecules out of the film. The porous nano silicon ion separation film has large hydrophilic area, the hydrophilic ions with smaller radius and hydrophilic molecules with smaller radius easily achieve relocation diffusion and have fast enrichment speed, and the porous nano silicon ion separation film is suitable for separation of organic and inorganic hydrophilic ions with smaller radius and Macromolecular substances with larger radius.