Polymer thin films containing fluorine are attracting much attention in various high-tech industries owing to their transparency, flexibility, and excellent water repellency. However, the generation of static electricity due to high electrical resistance limits their application. In this study, highly transparent and flexible Cu-plasma-polymerized fluorocarbon (PPFC) nanocomposite thin films that exhibit hydrophobicity and antistatic properties are proposed. These films, obtained using the mid-range frequency sputtering, exhibited a light transmittance of 84.2%, a water contact angle of 94.6°, and a sheet resistance of 1.2 × 10 Ω/□. Transmission electron microscopy and small angle X-ray scattering confirmed that Cu nanoparticles with an average size of 4-5 nm were distributed uniformly in the PPFC matrix. In repeated fatigue bending tests, the Cu-PPFC nanocomposite thin films exhibited excellent mechanical robustness and flexibility. Antiviral properties of the Cu-PPFC nanocomposite thin films were evaluated against influenza A virus, and the number decreased by 96.9% after 30 min. Carbon nanotube-Cu-polytetrafluoroethylene composite targets are advantageous for large-area coating and mass production because they can be applied in large-area sputtering and roll-to-roll processes. The transparency, charging characteristics, and water repellency can be easily controlled in Cu-PPFC nanocomposite thin films by controlling the sputtering power density according to the required product. Therefore, these films can be applied in various industries such as flexible displays, medical, automobiles, functional textiles, and aerospace.