The work aims to establish the uncertainty evaluation method for the determination of bisphenol S migration, so as to improve the experimental process management and reporting level of bisphenol S migration determination in can linings. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was used to detect the migration of bisphenol S in 4% acetic acid food simulants. According to the methods and steps in JJF 1059.1—2012 ''Evaluation and Representation of Determination Uncertainty'', the model for assessing the uncertainty was established. Based on the model, the main input variables affecting the determination uncertainty were analyzed to calculate the uncertainty components and evaluate the determination results. In this experiment, the determination uncertainty of bisphenol S migration in can linings was (2.25±0.302)mg/g, k=2. Uncertainty evaluation and analysis show that in this experiment, the measuring instrument component, calibration curve fitting component and standard solution component are the most important influencing factors.