A novel capillary electrochromatography method was developed by using a polymethacrylate ester based monolithic column for the simultaneous separation and determination of five nucleoside and purine compounds in urine. The porous monolithic column was first designed by mean of in situ copolymerizing stearyl methacrylate, trihydroxymethyl-propyl trimethylacrylate, and 2-acrylamido-2-methyl-1-propanesulfonic acid in a ternary porogenic solvent including cyclohexanol, 1,4-butanediol, and water. The performance and influence factors of the monolithic columns were investigated and evaluated by a CEC method. The five compounds including guanine, adenine, adenosine, cytidine, and N-6-methyladenosine were selected as analytes. Under the optimized condition of 6.0 mM phosphate buffer at pH 5.0 without ACN, five analytes were rapidly separated in 4 min with the high separation efficiency. The recoveries of spiked samples were ranged from 89.0 to 109.0% with RSDs less than 4.83%. Therefore, the proposed method could possibly provide for rapid separation and detection of the nucleoside and purine compounds in biomedicine sample.