A facile method to fabricate molecularly imprinted polymers (MIPs) on glass microspheres in a column was developed. The column was prepacked with glass microspheres, and then the prepolymerization mixture was injected into the interstitial volume of the column. The polymerization took place in situ and the column could be directly used for high-performance liquid chromatography after the template had been removed. The template consumption was reduced greatly because the prepolymerization mixture just filled the interstitial volume between the glass microspheres in the column. The MIPs obtained exhibited better kinetic properties, higher efficiency, and low back pressure of the column. Emodin imprinted polymers were prepared by this method and were used for solid-phase extraction.