The aerobic oxidation of cyclohexene is of great significance from the viewpoints of both fundamental and industry studies as it can transfer the petrochemical feedstock into valuable chemicals. In this research, gold nanoparticles were synthesized on the multi‐layer functionalized reduced graphene oxide. The surface of reduced graphene oxide (rGO) was modified with hydrophobic and hydrophilic layers to create the rGO with scattered hydrophilic positions. The gold nanoparticles were synthesized and immobilized simultaneously in small hydrophilic micro reactors in a mild condition. Characterization of synthesized nanocatalyst was confirmed with different techniques such as TEM, XRD, FT‐IR, and SEM. TEM images of synthesized catalyst show the gold nanoparticles have diameters less than 5 nm. Designed nanonanocatalyst was investigated for the selective liquid phase oxidation of cyclohexene with molecular oxygen in solvent free condition which after optimized conditions a maximum of 88% conversion and 91% selectivity was obtained.