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Procedures for discovering quality control markers from traditional Chinese medicines by the fingerprint-efficacy modeling were presented.Detailed chemometric methods used for fingerprint-efficacy relationship modeling were described.Applications of fingerprint-efficacy relationship labeled by chemometrics were tabulated.Challenges and future perspectives were discussed.Quality control (QC) is crucial for ensuring the safety and effectiveness of traditional Chinese medicines (TCMs). Due to extremely complicated phytochemical matrices and characteristic mode of “multi-component, multi-target, integrated adjustment”, discovering of QC markers from TCMs is a big challenge. Fingerprint-efficacy (FE) modeling method is currently proposed as an effective and reasonable attempt. This review summarizes the methodologies of FE modeling and applications in screening QC markers, meanwhile the future perspectives are also briefly discussed so as to provide inspiration and reference for follow-up study of FE relationship for TCMs.