Active ingredients discovery has always been a hot topic for the research of Chinese medicines (CMs). The component-effect relationship is one of the widely used strategies for finding herbal active ingredients. This article systematically reviewed component-effect relationship analysis in the application of active compo-nents discovery in CMs, including sampling and sample preparation, chemical finger-print establishment, pharmacological effect evaluation, and component-effect relationship analysis. The challenges to this method, such as the effects of dose–response relationship, data normalization, and the relationship analysis methods, were also discussed, which is helpful to well understand the method and improve the research quality.