Abstract: We performed an extensively targeting metabolomic detecting using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) to compare the secondary metabolites in Dang shen Codonopsis pilosula (Franch.) Nannf. from Shanxi and Gansu provinces. The findings showed that 161 secondary metabolites in 6 groups (phenolic acids, flavonoids, lignans and coumarins, alkaloids, terpenoids, others) were found from Dang shen in Changzhi city of Shanxi province and Dingxi city of Gansu province. There were 98 secondary metabolites which is differed significantly. In comparison to Dingxi city, 33 different secondary metabolites of Dang shen in Changzhi city had a greater relative content, whereas relative content of 65 different metabolites in Dingxi city was higher. Metabolic pathway enrichment analysis revealed that phenolic acids and flavonoids were significantly different in the secondary metabolites of Dang shen from different producing places. This may be one of the reasons for the difference in the quality of Dang shen in Shanxi and Gansu provinces. This work compared and analyzed the secondary metabolites of Dang shen from Dingxi city in Gansu province and Changzhi city in Shanxi province for the first time, which lays the foundation for further study on the quality of Dang shen.