The present invention relates to a method of preparing a hydrophobic metal oxide-silica composite aerogel having a high specific surface area and a low tap density and a hydrophobic metal oxide-silica composite aerogel prepared thereby. Thus, the preparation method may not only have excellent productivity and economic efficiency due to a relatively simpler preparation process and shorter preparation time than the related art, but may also prepare a hydrophobic metal oxide-silica composite aerogel having a high specific surface area and a low tap density.