The system for preparing silica aerogel comprises a raw material supply part transferring at least one raw material of de-ionized water, water glass, a surface modifier, an inorganic acid, and an organic solvent to a mixing part, the mixing part mixing the raw materials transferred from the raw material supply part to produce silica wet gel, a separating part separating at least one raw material of the raw materials from the mixture containing the silica wet gel transferred from the mixing part, a drying part drying the silica wet gel transferred from the separating part to produce the silica aerogel, a recovery part recovering a portion of the vaporized raw material of the raw materials used in at least one of the mixing part and the drying part, and a heat transfer part transferring heat to at least one of the mixing part and the drying part.