In this study， the differences in alkaloid composition and antioxidant activities in vitro were investigated based on plant wide targeted metabolomic techniques using the ‘Ningqicai No. 1’ goji leaves from three origins in Ningxia (Yinchuan， Zhongning， and Guyuan). The results showed that the alkaloid extracts of the samples from the three origins all had in vitro antioxidant activities. Among them， the scavenging ability of ABTS+ is Zhongning (35.4%) > Yinchuan (29.6%) > Guyuan (28.9%). The scavenging ability of superoxide anion is Yinchuan (84.8%) > Guyuan (83.9%) > Zhongning (82.1%). The total reduction capacity is Zhongning (0.46) > Guyuan (0.45) > Yinchuan (0.41). A total of 12 categories and 162 alkaloid metabolites were detected in the three regions. Under the screening conditions of multiple difference ≥ 2 or ≤ 0.5， P<0.05， and VIP ≥ 1， there were 53 significantly changed alkaloid differential metabolites in the comparison group between Yinchuan and Guyuan (including 21 up regulated and 32 down regulated)， 25 significantly changed alkaloid differential metabolites between Zhongning and Guyuan (including 16 up regulated and 9 down regulated)， and 59 different metabolites with significant changes between Yinchuan and Guyuan (including 31 up regulated and 28 down regulated). Five alkaloid metabolites with significant differences were identified through simultaneous comparison among the three production areas (dihydrocaffeioyl putrescine， panthenol mercaptoethylamine， wolfberry D， acetaminophen， and 3，4-dimethoxybenzamide). The KEGG database pathway enrichment analysis found that the five alkaloid metabolites with significant differences were mainly distributed in four metabolic pathways， namely metabolic pathway， biosynthesis of secondary metabolites， carbapenem biosynthesis， and pantothenate and CoA biosynthesis pathways. This study provides a theoretical basis for nutritional exploration of ‘Ningqicai No.1’ goji leaves from different regions in Ningxia.