Black wolfberry is a commonly cultivated woody plant in China, and is rich in nutrients that are beneficial for human. To characterize the endogenous metabolite differences among black wolfberry fruits grown in different geographical regions, mass spectrometry-based metabolomic and lipidomic analyses were performed in black wolfberry grown in nine locations throughout five provinces in China, from which 204 primary and specialized metabolites, and 267 lipids were identified in their fruits. Three samples from Alxa Left Banner, Jinta, and Minqin showed dramatically altered metabolite profiles, displaying higher levels of phenolic acids, soluble sugars and flavonoids, but lower levels of tricarboxylic acid cycle intermediates and aromatic amino acids. Moreover, the lipid profile of the Alxa Left Banner sample was strikingly distinct from all other samples, with high levels of monogalactosyl diacylglycerol and sulfoquinovosyl diacylglycerol, which are positively correlated with their anti-inflammatory capacities. These findings thus prompt for further studies on black wolfberry fruit for their health benefits.