The present invention relates to a method of preparing a high hydrophobic silica aerogel having a low tap density and a hydrophobic silica aerogel prepared thereby. The method of preparing a hydrophobic silica aerogel according to the present invention may have good productivity and economic efficiency, because preparation time is reduced by simultaneously performing surface modification and solvent substitution in a single step, and may control a degree of hydrophobicity of the prepared silica aerogel by controlling a surface modification reaction by including a step of adding ammonium hydroxide. Thus, a hydrophobic silica aerogel having excellent physical properties, such as tap density and specific surface area, as well as high hydrophobicity obtained by controlling the degree of hydrophobicity may be prepared.