The present invention relates to a method of preparing a hydrophobic metal oxide-silica composite aerogel, in which a degree of hydrophobicity may be controlled while having a high specific surface area and a low tap density, and a hydrophobic metal oxide-silica composite aerogel prepared thereby. The preparation method according to the present invention 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 perform an effective surface modification reaction by using a small amount of a surface modifier. Thus, since the surface modification reaction may be easily performed by using only a very small amount of the surface modifier, a hydrophobic metal oxide-silica composite aerogel containing about 1 wt% to 2 wt% of carbon may be prepared.
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