Objective: To improve the accuracy and validity of the measurement data of solvent residues in food packaging paper. Methods: Taking the HS GC-MS measurement system as the research object, variation sources in the measurement process was separated by using the measurement system analysis, and the traditional control chart and EWMA control chart of repeatability and reproducibility were established respectively to effectively monitor the detection error of the measurement system. Results: ① HS GC/MS had high measurement accuracy, with GRR of about 9.76%, and the gauging ability of the measurement system was relatively good. ② Through the combination of periodic measurement system analysis and control chart method, the effective separation and monitoring of repeatability and reproducibility variance components can be realized. ③ The repeatability can be monitored in real time through the daily gauging data, which was helpful to find the fault of measurement equipment in time and ensure the reliability of gauging results. ④ EWMA chart of repeatability can give early warning of measuring equipment fault faster than traditional control chart. Conclusion: Separating and monitoring variation sources of the measurement system by using variance analysis method can effectively ensure the stability of HS GC-MS equipment and improve the effectiveness of solvent residue detection.