Microscale separations, e.g., capillary electrophoresis (CE) and capillary electrochromatography (CEC), are powerful analytical techniques that provide fast and efficient separation with low consumption of sample and reagent. Due to their versatility and high efficiency, CE and CEC have attracted great interest of analysts in the analysis of phytochemicals in Chinese medicines. And they have become alternative methods to the widely used high-performance liquid chromatography. In this study, CE and CEC analysis of flavonoids from Epimedium and licorice, as well as nucleosides and nucleobases, were investigated. The effect of stability of internal standard on quantitative determination and peak suppression technique for quantification of overlapping peaks were also studied. In addition, preliminary investigation on hypercrosslinked porous poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) and poly(4-methylstyrene-co-vinylbenzyl chloride-codivinylbenzene) monolithic columns for CEC analysis of small molecules were also performed. The major achievements of this study are summarized as follows: (1) A capillary zone electrophoretic method for simultaneous determination of 15 flavonoids, including epimedin B, epimedin A, hexandraside F, epimedin C, icariin, sagittatoside B, sagittatoside A, hexandraside E, 2"-O-rhamnosyl icariside II, baohuoside VII, baohuoside I, caohuoside C, epimedoside C, baohuoside II and kaempferol-3-O-rhamnoside, in different species of Epimedium were developed, and the effect of stability of internal standard on quantification was also investigated. (2) CEC methods for simultaneous determination of flavonoids in Epimedium and licorice using packed C18 capillary column were developed, respectively. The influence of relevant parameters such as buffer concentration, pH and proportion of acetonitrile were investigated and optimized. Peak suppression technique was used for the quantification of the overlapping peaks, isoliquiritin and ononin, based on the differences between their UV absorption spectra. (3) The utility of hypercrosslinked poly(styrene-co-vinylbenzyl chloride-codivinylbenzene) and poly(4-methylstyrene-co-vinylbenzyl chloride-codivinylbenzene) monolithic columns for CEC separation was demonstrated for the first time. The separation of alkylbenzenes, flavonoids from Epimedium, as well as nucleosides and nucleobases was also investigated. Although alkylbenzenes were successfully separated, the separations of flavonoids from Epimedium and nucleosides and nucleobases using these columns were not good. Further efforts should be made to improve the CEC separation of phytochemicals using the monolithic columns. In summary, microscale separations including CE and CEC analysis of selected phytochemicals in Chinese medicines were developed and investigated, some of which were studied for the first time. This study is helpful for the application of CE and CEC for quality control of Chinese medicines.