A fluorine-silicon polymer (PFAMS) with pendant perfluoroalkyl and reactive epoxy groups was firstly synthesized by bulk polymerization (Si-H additional reaction) of polymethyltrifluoropropylsiloxane (PFHMS), allylpolyoxyethylene ether (AGE) and perfluorooctyl ethylene (PFOE). Then amino-functionalized nano silica (KH550-SiO2) was prepared via sol-gel method by 3-aminopropyltriethoxylsilane (KH550) and tetraethyl orthosilicate (TEOS). Finally novel fluorosiloxane polymer/silica hybrid nanocomposites (PFAMS-SiO2) were fabricated through graft copolymerization method by the above two chemicals, PFAMS and KH550-SiO2 and super-hydrophobic cotton fabric was also constructed with contact angle of water on its surface 160.91° through immersing-padding-baking processes. Chemical structure, thermal performance, micro-morphology and hydrophobic property of the hybrid materials and film were investigated by Fourier Transform Infrared Spectrum (FT-IR), Thermogravimetric Analyzer (TGA), X-ray photoelectron spectroscopy (XPS), Scanning electron microscopy (SEM) and Static contact angle analyzer, respectively. Results show that a hydrophobic film and many lotus-leaf-like micro-nano scale tubercles are coated on the surface of cotton fabrics.