[Objective] To achieve good internal quality control of determination of decamethylammonium chloride and benzalkonium chloride residues in drinking water by high performance liquid chromatography tandem mass spectrometry, and to promote the improvement of detection methods. [Methods] A mathematical model and fishbone diagram were established to evaluate the introduced uncertainty components, and the combined standard uncertainty and expanded uncertainty were calculated. [Results] Under the inclusion factor k=2, and the decamethylammonium chloride and benzalkonium chloride residue in drinking water samples was 4.3 μg/L and 4.7 μg/L and their expanded uncertainty U was 0.52 μg/L and 0.48 μg/L, respectively. [Conclusion] The uncertainty in determining the two disinfectants with high performance liquid chromatography tandem mass spectrometry mainly comes from the preparation of the series standard solutions, determination repeatability, and instrument calibration, etc.