A high-performance capillary electrophoresis (CE) with electrochemical detection (ED) method was developed for the determination of the pharmacologically active ingredients in Erigeron breviscapus (Vant.) Hand-Mazz. and its extract phytopharmaceuticals in this work. Under the optimum conditions, nine analytes, baicalein, naringenin, scopoletin, kaempferol, apigenin, scutellarin, luteolin, caffeic acid and protocatechuic acid were separated within 24 min in a borax buffer (pH 8.7). Notably, excellent linearity was obtained over two orders of magnitude with detection limits ( S/ N = 3) ranged from 1.0 × 10 −7 g/mL to 5.6 × 10 −7 g/mL for all nine analytes. This method was successfully used in the analysis of E. breviscapus (Vant.) Hand-Mazz. and its phytopharmaceuticals with a relatively simple extraction procedure, and the assay results were satisfactory.