Multifunctional coatings with superhydrophobicity, high transparency, thermal stability, flexibility, and ultralow refractive index have been investigated for many years. They have promising applications in industries such as in electronic and optical devices, photonic materials, and templates for fabricating biological and chemical sensors. However, the relatively complex preparation technology of these coatings or difficult to possess these properties simultaneously are still the main factors that limit their wide application. In this paper, we report a facile atmospheric approach to create transparent multifunctional raspberry-like particulate coatings with a low refractive index, which were obtained via one-pot base-catalyzed sol-gel process using tetraethyl orthosilicate (TEOS) and 1H, 1H, 2H, 2H-perfluorooctyltrimethoxysilane (POTS) as co-precursors. The excellent superhydrophobicity, mechanical flexibility, self-cleaning property, thermal and chemical stability of the as-fabricated coatings were demonstrated. The refractive indices of coatings can be easily tuned at a range of 1.07–1.16. Particularly, the resulted samples on the K9 glasses exhibited superhydrophobicity with a water contact angle (WCA) of 162° when the scale ratio of the POTS and TEOS was 1.0. The superhydrophobicity of the as-prepared coatings could last for more than half a year under indoor condition, demonstrating the long stability of the superhydrophobicity. Furthermore, we demonstrated that this simple efficient method could be extended to different substrates, including K9 glass, Polyvinyl chloride (PVC), stainless steel, aluminum alloy, and gingko leaf, to achieve superhydrophobicity. Interestingly, the superhydrophobicty of the coatings transferred to superhydrophilicity (WCA < 5°) by calcination at 500 °C, which resulted in a good antifogging property. Moreover, the coatings were not sensitive to the strong acid (pH = 1) and kept their superhydrophobic state for a long time (over 80 min). The coatings on PVC retain their excellent water-repellency after multiple bending cycles. Also, these coatings produced a fair transparency consisting of more than a 2.0% increase in optical transmittance in the visible-near infrared spectral range. Our study is promising building blocks for large-area, mechanical flexible, ultralow-refractive-index, superhydrophobic and environment-resistant surfaces.