This study aimed to understand the difference in metabolites of three major jujube cultivars from north Shaanxi, in order to provide a reference for quality analysis and functional evaluation of jujube fruit. The metabolites in Qingjian Muzao, Jiaxian Youzao and Yanchuan Goutouzao were determined and compared by wildly targeted metabonomics based on ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and multivariate statistical analysis. A total of 462 metabolites, belonging to 15 categories, were identified across the three cultivars, and a significant difference in the contents of metabolites was observed among them. Totally 36 differential metabolites between Jiaxian Youzao and Qingjian muzao were identified. In addition, 193 and 204 differential metabolites were identified in Yanchuan Goutouzao compared with qingjian Muzao and Jiaxian Youzao, respectively. KEGG pathway enrichment analysis of the differential metabolites indicated that amino acid metabolism and phenylpropanoid biosynthesis pathway were more active in Yanchuan Goutouzao, while flavonoid biosynthesis pathway was more active in Qingjian Muzao and Jiaxian Youzao. Amino acids such as tryptophan, phenylalanine, tyrosine, histidine, valine, threonine, leucine, isoleucine, sinapic acid, p-coumaric acid and cinnamic acid, as well as phenolic acids such as syringin were accumulated in larger quantities in Yanchuan Goutouzao, while flavonoids such as myricitrin, astragalin, aromadendrine, 4,2’,4’,6’-tetrahydroxychalcone and butin were accumulated in larger quantities in Qingjian Muzao and Jiaxian Youzao. At the metabolic level, it was found that qingjianmuzao had a closer genetic relationship with Jiaxian Youzao, but further relationship with Yanchuan Goutouzao. Qingjianmuzao and Jiaxian Youzao had higher medicinal value, while Yanchaun Goutouzao had more prominent nutritional quality and taste.