A method of manufacturing a hydrophobic aerogel using a process of reforming a wet gel into a hydrophobic aerogel by a generally known normal temperature and pressure method, including: directly providing a reticular basket in a reactor; introducing a wet gel into the basket; providing an ultrasonic generator under the reactor to emit ultrasonic waves; and providing a nitrogen injection unit under the ultrasonic generator to inject nitrogen into the reactor upwards, thereby accelerating a reaction. An apparatus for manufacturing a hydrophobic aerogel, including: a reactor for reforming a wet gel into a hydrophobic gel, the reactor being provided therein with a support to allow a basket to be disposed therein, an ultrasonic generator which is provided under the reactor; and a nitrogen injection unit which is provided under the ultrasonic generator.