We report on the high-throughput production of heterogeneous catalysts of RuO2-deposited graphene using a hydrodynamic process for selective alcohol oxidation. The fluid mechanics of a hydrodynamic process based on a Taylor–Couette flow provide a high shear stress field and fast mixing process. The unique fluidic behavior efficiently exfoliates graphite into defect-free graphene sheets dispersed in water solution, in which ionic liquid is used as the stabilizing reagent to prevent the restacking of the graphene sheets. The deposition of RuO2 on a graphene surface is performed using a hydrodynamic process, resulting in the uniform coating of RuO2 nanoparticles. The as synthesized RuO2/IL–graphene catalyst has been applied efficiently for the oxidation of a wide variety of alcohol substrates, including biomass-derived 5-hydroxymethylfurfural (HMF) under environmentally benign conditions. The catalyst is mechanically stable and recyclable, confirming its heterogeneous nature.