The present invention relates to a method for preparing a highly hydrophobic silica aerogel having a low tapped density, and to a hydrophobic silica aerogel prepared therefrom. The method for preparing a hydrophobic silica aerogel, according to the present invention, has a short preparation time by enabling performing surface modification and solvent substitution simultaneously in one step, and thus may have excellent productivity and economic efficiency, and enables controlling a surface modification reaction by including a step for adding ammonium hydroxide, thereby enabling controlling the hydrophobicity level of the silica aerogel being prepared, thus enabling the preparation of a hydrophobic silica aerogel that not only has excellent physical properties such as tapped density and specific surface area, but also has a high hydrophobicity by means of having the hydrophobicity level thereof controlled.