Pressurized capillary electrochromatography (pCEC) combines capillary electrophoresis (CE) with high performance liquid chromatography (HPLC), resulting in high separation efficiency, high selectivity, high resolution and fast speed. In addition, it provides a solvent gradient capability. Based on pCEC, a two-dimensional chromatography was constructed using micro strong cation exchange liquid chromatography and reversed phase pressurized capillary electrochromatography (micro-SCXLC/RP-pCEC) for the analysis of Cortex Phellodendri extract. A sample was separated by the first dimensional SCX column with a linear salt gradient elution into 11 plugs. Each plug was collected and injected into the second dimensional RP-pCEC column with a linear gradient for further separation. Compared with one-dimensional liquid chromatography, it has higher resolution and larger peak capacity. The two-dimensional chromatographic system is suitable for the separation and analysis of complex samples.