In order to properly improve the integrity and reliability of the results, the LC-MS/MS method was used to determine the discrepancy of the detection results of papaverine, narcotine, thebaine in soup flavor seasoning powder. This paper based on “DB 31/2010—2012 of local standards for food safety, the Determination of Papaverine, Morphine, Narcotine, Codeine and Thebaine in Hot Pot Food by Liquid Chromatography-Tandem Mass Spectrometry”, analyzed the residue results of papaverine, narcotine, thebaine in soup flavor seasoning powder and the sources of the uncertainty of measurement. It also synthesized the total uncertainty. The results showed that the synthesis of relative standard uncertainty for papaverine, narcotine, thebaine were 0.475, 0.575, 1.897, respectively. The source was mainly comes from configuration of the standard solution, standard curve and experimental repeatability.