In conclusion, we have developed a highly efficient magnetic catalyst graphene encapsulated thin layer Ni@C for highly active hydrogenation of acetophenone to phenylethanol and successfully applied it in a flow reactor with an excellent conversion rate and selectivity. The oxidation step, pyrolysis temperature, and solvent have an impact on the catalytic activity and product selectivity of the catalysis. We selected Ni@C-700-EtOH with the lowest hydrogenation activity of acetophenone among the prepared catalysts in batch reactor to carry out the hydrogenation reaction in the continuous flow reactor to highlight the advantages of the flow reactor which can significantly improve mass and heat transfer. Hydrogen pressure, reaction temperature, and reaction liquid flow rate have significant effects on the hydrogenation conversion rate and selectivity. In the final screening and optimization of the industrially adapted reaction conditions, the continuous hydrogenation of acetophenone was carried out for 48 hours to test the recyclicity of the catalyst. After 48 hours, the conversion rate and selectivity remained high. Compared with batch reactors, under optimized conditions, the catalytic activity of acetophenone hydrogenation in continuous flow reactor has been greatly improved. In short, the active catalyst loaded with a graphene shell has excellent stability which can be successfully used in advanced industrially applicable flow reactor by simply switching different control valves for the hydrogenation of acetophenone to benzene phenylethanol with excellent yields.