The introduction of super-hydrophobicity into the field of photocatalysis has attracted the attention of many researchers nowadays. Here, CuO nanowires were synthesized via thermal oxidation method. The flower-like ZnO nanostructures were self-assembled with CuO nanowires by hydrothermal growth method. The functionalized super-hydrophobic CuO/ZnO layered composite nano-photocatalyst was obtained though polydimethylsiloxane (PDMS) grafting. We analyzed the effects of zinc sources, hydrothermal reaction time, solution concentration and surfactant concentration on the properties of the composite nano-photocatalyst. FESEM micrographs revealed CuO/ZnO layered composite nanostructures, which were composed of CuO nanowires with uniform morphology and carnation-like ZnO nanoflowers. XRD spectrum showed CuO/ZnO layered composite nano-photocatalyst possessed pure CuO phase and the wurtzite structure of ZnO. UV–vis spectrum manifested that the composite nanostructures had desired light absorption for ultraviolet light band and the contact angle (CA) results confirmed the successful modification of super-hydrophobic functionalization. After the modification of PDMS, the CuO/ZnO layered composite nano-photocatalyst prepared with the optimal conditions shows desired photocatalytic properties and super-hydrophobicity. The stable super-hydrophobic property after photocatalytic degradation is expected to improve self-cleaning and broaden the application field of photocatalyst.