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Nanoscale surface roughness has conventionally been induced by using complicated approaches; however, the homogeneity of superhydrophobic surface and hazardous pollutants continue to have existing challenges that require a solution. As a prospective solution, a novel bubbled-structured silica nanoparticle (SiO2) decorated electrospun polyurethane (PU) nanofibrous membrane (SiO2@PU-NFs) was prepared through a synchronized electrospinning and electrospraying process. The SiO2@PU-NFs nanofibrous membrane exhibited a nanoscale hierarchical surface roughness, attributed to excellent superhydrophobicity. The SiO2@PU-NFs membrane had an optimized fiber diameter of 394 ± 105 nm and was fabricated with a 25 kV applied voltage, 18% PU concentration, 20 cm spinning distance, and 6% SiO2 nanoparticles. The resulting membrane exhibited a water contact angle of 155.23°. Moreover, the developed membrane attributed excellent mechanical properties (14.22 MPa tensile modulus, 134.5% elongation, and 57.12 kPa hydrostatic pressure). The composite nanofibrous membrane also offered good breathability characteristics (with an air permeability of 70.63 mm/s and a water vapor permeability of 4167 g/m2/day). In addition, the proposed composite nanofibrous membrane showed a significant water/oil separation efficiency of 99.98, 99.97, and 99.98% against the water/xylene, water/n-hexane, and water/toluene mixers. When exposed to severe mechanical stresses and chemicals, the composite nanofibrous membrane sustained its superhydrophobic quality (WCA greater than 155.23°) up to 50 abrasion, bending, and stretching cycles. Consequently, this composite structure could be a good alternative for various functional applications.