Background <p><i>Ziziphus jujuba var. spinosa,</i> commonly known as ‘wild jujube,’ is a significant medicinal and edible plant. While the value of its seeds and pulps is well established, the potential of its leaves has been largely neglected<i>.</i></p> Methods <p>In this study, we determined the contents of basic chemical components—including total flavonoids, total phenolics, and total saponins—in the leaves, pulp, and seeds of <i>Z. jujuba var. spinosa</i>, and we evaluated their antioxidant activities. In addition, widely targeted metabolomics combined with high-performance liquid chromatography (HPLC)-based targeted validation was employed to systematically compare the metabolite profiles.</p> Results <p>The three organs exhibited distinct metabolic functional differentiation. Leaves displayed the highest contents of total flavonoids, total phenolics, and total saponins, along with the strongest in vitro antioxidant activity. The characteristic accumulation of flavonoid glycosides, such as rutin and isoquercitrin, and of triterpene saponins, such as pedunculagin, may be associated with defense functions. Pulp accumulated significant amounts of soluble sugars and organic acids, such as citric acid, and contained moderate levels of flavonoids. Seeds functioned as a protein reservoir and accumulated C-glycosylated flavonoids and dammarane-type triterpene saponins. KEGG pathway enrichment analysis showed that flavonoid biosynthesis, phenylpropanoid biosynthesis, and terpenoid backbone biosynthesis are the core pathways driving this organ-specific metabolic differentiation. This study systematically suggests, for the first time from a metabolomics perspective, the “defense–dispersal–reserve” functional differentiation pattern among the leaves, pulp, and seeds of <i>Z. jujuba</i> var. <i>spinosa</i>. These findings provide a scientific basis for developing the leaf, a nontraditional organ, as a high-value antioxidant resource and lay a theoretical foundation for comprehensive whole-plant utilization.</p>