Construction of hybrid three-dimensional (3D) hierarchical nanostructures via self-assembly of organic and inorganic compounds have recently attracted immense interest from scientists due to their unique properties and promise in a large range of applications. In this article, hybrid flower structures were successfully constructed by self-assembly an antibiotic, kanamycin, with Cu2+. The flower-like morphology was observed by scanning electron microscopy, to be approximately 4 µm in diameter and about 10 nm in thickness. FTIR spectroscopy and X-ray diffraction confirmed the antibiotic-inorganic hybrid structure was uniform composition, and showed crystallinity due to ordered self-assembly. The hybrid flowers showed high photocatalytic activity towards degradation of methyl blue during 240 minutes under visible light irradiation. A possible mechanism of photocatalytic activity was also proposed, that exposes the inherent advantages in using antibiotic-inorganic hybrid flowers as photocatalysts, where self-assembly can be used to generate active, high surface area structures for photodegradation of pollutants.