Monodisperse iron oxide nanocrystals and organic solvents were utilized as coporogens in monolithic poly(glycidylmethacrylate-co-ethylene glycol dimethacrylate) capillary columns to afford stationary phases with enhanced electrochromatographic performance of small molecules. While the conventional monoliths using organic solvents only as a porogen exhibited poor resolution (Rs) <1.0 and low efficiency of 40 000-60 000 plates/m, addition of a small amount of nanocrystals to the polymerization mixture provided increased resolution (Rs > 3.0) and high efficiency ranged from 60 000 to 100 000 plates/m at the same linear velocity of 0.856 mm/s. It was considered that the mesopores introduced by the nanocrystals played an important role in the improvement of the monolith performance. This new strategy expanded the application range of the hydrophobic monoliths in the separation of polar alkaloids and narcotics. The successful applications demonstrated that the glycidyl methacrylate based monoliths prepared by using nanocrystal template are a good alternative for enhanced separation efficiency of small molecules.