Five common food preservatives were analyzed by capillary electrochromatography, utilizing a methacrylate ester-based monolithic capillary as separation column. In order to optimize the separation of these preservatives, the effects of the pore size of the polymeric stationary phase, the pH and composition of the mobile phase on separation were examined. For all analytes, it was found that an increase in pore size caused a reduction in retention time. However, separation performances were greatly improved in monolithic columns with smaller pore sizes. The pH of the mobile phase had little influence on separation resolution, but a dramatic effect on the amount of sample that was needed to be electrokinetically injected into the monolithic column. In addition, the retention behaviors of these analytes were strongly influenced by the level of acetonitrile in the mobile phase. An optimal separation of the five preservatives was obtained within 7.0 min with a pH 3.0 mobile phase composed of phosphate buffer and acetonitrile 35:65 v/v. Finally, preservatives in real commercial products, including cold syrup, lotion, wine, and soy sauces, were successfully determined by the methacrylate ester-based polymeric monolithic column under this optimized condition.