Polymethylsilsesquioxane (PMSQ) aerogels obtained from methyltrimethoxysilane (MTMS) are well-known high-performance porous materials. Highly transparent and hydrophobic PMSQ aerogel would play an important role in transparent vacuum insulation panels. Herein, the co-precursor approach and supercritical modification method were developed to prepare the PMSQ aerogels with high transparency and superhydrophobicity. Firstly, benefiting from the introduction of tetramethoxysilane (TMOS) in the precursor, the pore structure became more uniform and the particle size was decreased. As the TMOS content increased, the light transmittance increased gradually from 54.0% to 81.2%, whereas the contact angle of water droplet decreased from 141° to 99.9°, ascribed to the increase of hydroxyl groups on the skeleton surface. Hence, the supercritical modification method utilizing hexamethyldisilazane was also introduced to enhance the hydrophobic methyl groups on the aerogel’s surface. As a result, the obtained aerogels revealed superhydrophobicity with a contact angle of 155°. Meanwhile, the developed surface modification method did not lead to any significant changes in the pore structure resulting in the superhydrophobic aerogel with a high transparency of 77.2%. The proposed co-precursor approach and supercritical modification method provide a new horizon in the fabrication of highly transparent and superhydrophobic PMSQ aerogels.