The present invention relates to a method of preparing a high hydrophobic silica aerogel having a high specific surface area and 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, gelation, 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, the preparation method according to the present invention and the hydrophobic silica aerogel are suitable for industries that need the method and the hydrophobic silica aerogel, particularly, industries that need a silica aerogel having high hydrophobicity or industries that need a silica aerogel having various degrees of hydrophobicity.