Under microwave radiation and using trimethyl chlorosilane as modifier, hydrophobic SiO2 aerogel was prepared through fractional hydrophobic modification and ambient pressure drying of the raw material, tetraethoxysilane (TEOS), in the process of sol-gel and acid-base catalysis. Hydrophilic SiO2 aerogels were also prepared using the microwave method and water bath heating method. The SiO2 aerogels prepared using the three methods, including their morphology and chemical composition, were analyzed and compared using scanning electron microscopy, Brunauer-Emmett-Teller analysis method, Fourier transform infrared spectroscopy, X-ray diffraction, and themogravimetric-differential scanning calorimetry. The results indicate that by adopting the microwave reaction, the specific surface area of the SiO2 aerogels was effectively increased and the structure of the internal nanoscale pores of petal-coated shape was found to exist under the dense external surface of the SiO2 aerogels. Thermal stability of the hydrophobic SiO2 aerogels prepared through fractional modification assisted by the microwave method was increased with the hydrophobic angle at153°, which showed super hydrophobicity.