A method of separating oil-soluble pigment and water-soluble pigment from natural material using aerogels characterized in comprising the steps of: (A) immersing a natural material in a leaching solvent to extract a pigment; (B) mixing the leaching solution from which pigment is extracted in step (A) with aerogel to adsorb oil-soluble pigment to aerogels; (C) separating oil-soluble pigment adsorbed on the surface of aerogel in step (B); (D) drying and concentrating the pigment separated in step (C), enhancing a method of separating from natural material the initial substance for pharmaceuticals, food, cosmetics, etc. facilitating a safer and more efficient production process compared to the conventional separation method.