IntroductionThe quality evaluation of Coptidis rhizome (CR) is attributed to the origin and processing method, and this strategy of ignoring the bioactive components usually leads to biased quality analysis, which is difficult to indicate the clinical efficacy.ObjectivesIn order to evaluate the quality level of different species of CR, we collected 20 batches of CR and investigated the fingerprint‐effect relationship.MethodsHigh‐performance liquid chromatography (HPLC) fingerprints of CR were established, and the fingerprint‐effect relationship was explored using cluster analysis, principal component analysis, Pearson correlation analysis, grey relation analysis, and partial least squares regression.ResultsWe have identified a total of 10 common peaks (1–10) with similarity scores above 0.96. The study on the relationship between spectra and potency further showed that the contents of peaks 8, 9, and 10 are potential key components. And based on a previous study, a method of one measurement and multiple evaluations of CR was established to achieve the goal of simplifying the analytical process and reducing costs.ConclusionThrough a combination of fingerprint analysis, antioxidant activity evaluation, fingerprint‐efficacy relationship analysis, and simultaneous quantification of multiple components, a CR quality control index and method have been selected and established, which can also provide a more comprehensive quality evaluation for traditional Chinese medicine.