An ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) was introduced as dynamic coating of a silica monolithic column for capillary electrochromatography of phenols and nucleoside monophosphates. The run-to-run and column-to-column repeatability of migration time for six phenols were satisfactory on this column with relative standard deviation values less than 0.90 and 4.31%, respectively. Anodic electroosmotic flow (EOF) was observed, which increased with the increase of [BMIM][BF4] concentration within 120 mM and when [BMIM][BF4] concentration was above 120 mM, EOF leveled off due to the saturation of [BMIM][BF4] on the monolith. Efficient separation of phenols and nucleoside monophosphates on this dynamically coated monolithic column was obtained, compared with a dynamically coated fused-silica column and unmodified silica monolithic column. The retention behavior of uncharged phenols is mainly manipulated by hydrophobic interactions due to the presence of butyl groups, and that of nucleoside monophosphates is governed by the electrostatic attraction mechanism based on the interaction between positively charged [BMIM][BF4] moieties and negatively charged phosphate groups. In addition, silica matrix also contributes to the separation resolution.