Capillary electrophoresis (CE) presents a promising possibility for analyzing traditional Chinese medicine (TCM) due to its low reagent consumption, high analysis speed, and enhanced efficiency. Herein we review the employment of CE for analyzing the effective components in TCM and identifying TCM via a fingerprint. Furthermore, we discuss the application of state-of-the-art capillary electrophoresis modes for screening enzyme inhibitors and investigating the interactions between TCM and plasma proteins. The review concludes with recommendations for future studies and improvements in this field of research. The general development trend identified in this review indicates that the application of CE has significantly improved TCM assay performance.