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• Amino acids, nucleosides, nucleobases, sugars and protein in goji were analyzed. • Nutritional component profiles of goji from different regions were compared. • The regions located in Hetao plain produced goji with similar chemical profile. • Fructose and glucose are the main markers to distinguish goji from different areas. Goji berries are used as functional food for hundreds of years in Asia, Europe, North America and Austria, and are popular for nutritive properties in global. Commercial Goji berries are mainly produced in Ningxia, Xinjiang, Gansu, Qinghai and Inner Mongolia of China. However, the Goji berries produced in these regions exhibited different appearance and taste. Thus, characterization of the nutritional components in Goji berries produced in these regions could provide the guidance for application of them. In this study, 94 samples were collected, and a total of 20 amino acids, 17 nucleosides and nucleobases, 4 sugars and protein were determined by UHPLC-MS/MS, HPLC-ELSD or UV, and the variation was illustrated through heatmap clustering analysis, PCA and PLS-DA. The results showed that Goji berries from Xinjiang were rich in protein than the samples from other regions; those from Gansu and Ningxia were rich in amino acids, nucleosides and nucleobases; and those from Jiuquan of Gansu and Qinghai were rich in sugars. Heatmap clustering and PCA analysis results showed that all the samples exhibited a significant spatial aggregation, and the producing regions located along the Yellow River (belonging to the Hetao plain) produced Goji berries with the similar chemical profile. Additionally, PLS-DA analysis results showed that fructose and glucose were the predominant markers to distinguish Goji berries from different producing regions. [ABSTRACT FROM AUTHOR]