Objective:To establish an ion chromatography method for the determination of methane sulfonic acid in betahistine me-sylate and evaluate the uncertainty in the measurement. Methods: An ion chromatographic column IonPac AS11-HC ( 25 mm × 4. 0 mm,5 μm) was used with 12 mmol·L-1 NaOH as the eluent and an electrical conductivity detector with the suppressor of 30 mV. Results:The results showed that methane sulfonic acid could be detected without any interference. The calibration curve was linear within the range of 10-30 μg·ml-1(r=0.999 9)and the LOQ was 0.116 μg·ml-1. The average recovery was 100.8% (RSD=1. 2%, n=9). Based on the results of experiments, the influencing factors of uncertainty in the measurement were quantitatively eval-uated. The expanded uncertainty was obtained. Conclusion:The method is simple, accurate and selective. It can be used for the de-termination of methane sulfonic acid in betahistine mesylate. Based on the evaluation of uncertainty, the analysis can help reduce the uncertainty in the measurement and improve the accuracy and reliability of the determination.