Objective: To analyze the differences of goji flavonoids from different origins from the perspective of proteomics. Methods: The protein differences of goji berries from different origins were explored by tandem mass tag (TMT) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology in Ningxia， Qinghai and Gansu. Results: A total of 716 differential expressed proteins(DEPs)， and a total of four metabolic pathways associated with flavonoids were found in the KEGG pathway， and the phenylpropane biosynthesis pathway was significantly enriched in all three comparison groups (P < 0.05)， indicating that the phenylpropane biosynthesis pathway might make a greater contribution to the synthesis of goji flavonoids. Further screening of 24 key differentially expressed proteins related to flavonoid synthesis， it was found that phenylalanine ammonia-lyase (PAL)， cinnamic acid 4-hydroxylase (C4H)， chalcone isomerase(CHI)， chalcone synthase (CHS)， etc. might be important DEPs for the biosynthesis of flavonoids in Ningxia， Qinghai and Gansu. Conclusion: The differential proteins related to the biosynthesis of goji flavonoids were identified from the protein level， and the anabolic pathway of goji flavonoids was preliminarily speculated， which laid a foundation for exploring the differences in the biosynthesis of goji flavonoids in different origins.