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A multi-variate digital fingerprint profile of fruit juice essence sample was established to evaluate the sample quality stability and distinguish sample groups using the combination of HPLC-DAD spectrum and UPLC-MS spectrum, which were collected to characterize the quality characteristics of flavor substances. [Display omitted] • A multivariate digital fingerprint was established with combination of HPLC-DAD and UPLC-MS/MS spectra. • The comprehensive HPLC fingerprint data was used to characterize the quality characteristics of each flavor substances. • The PCA model and CA model were built to evaluate the application of comprehensive fingerprint. • The proposed fingerprints method presented itself the potential application prospects in food industry. Quality control problem of essence and spices has always been the focus of food chemists in recent years. In this study, a multi-variate digital fingerprint profile of fruit juice essence sample was established using the combination of HPLC-DAD spectra and UPLC-MS spectra, which were collected to obtain the information about organic acids, polyphenols, sugars and sugar alcohols of the samples. The stability, reliability and repeatability of the combined fingerprinting method were verified in the work. A total of 36 markers in the established fingerprint were common (20 compounds were confirmed) belonging to different classes: organic acids, polyphenols, sugars, sugar alcohols, and other miscellaneous compounds. Those chromatographic peaks that significantly affect the quality of apple juice flavor were screened from principal component analysis (PCA). Moreover, PCA and cluster analysis of the proposed combined fingerprint gave the better evaluation of the sample quality stability and distinguish sample groups than the fingerprint from single data, which demonstrated its great significance to the quality control of fruit juice samples. [ABSTRACT FROM AUTHOR]