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This study analyzed the differential composition between from concentrate (FC) and not from concentrate (NFC) bayberry juices by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS). NFC and FC bayberry juice were distinguished from each other by orthogonal partial least squares discriminant analysis, and 9 compounds that significantly differed in abundance between them were selected and identified according to the variable importance in the projection and the fold-change. By comparison, the content of antioxidant active components such as 4-sulfobenzoate, 5-methyltetrahydrofolic acid, cyanidin, daphnoretin, xanthotoxol and isoxanthopterin in FC bayberry juice were relatively low, whereas the bitter substances (neohesperidin, hesperidin and quercetin-3-O-neohesperidin) were relatively high. Metabolic pathways were analyzed on account of differential metabolites and five metabolic pathways with great differences were identified, among which phenylalanine metabolism, biosynthesis of flavonoids and flavonols were the key metabolic pathways of different metabolites in NFC and FC bayberry juice. This study revealed the difference of metabolites between NFC and FC bayberry juice, which provided theoretical reference for the processing and identification of NFC bayberry juice.