An ultra-high performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC-MS/MS) method was established for the determination of six quaternary ammonium disinfectant residues in milk-containing food for special medical purposes. The sample was extracted with 80% acetonitrile in water and the extract was separated on a RRHD Eclipse Plus C18 column, detected in the positive ion mode using an electrospray ionization source with multiple reaction monitoring (MRM), and quantified by matrix-matched standard calibration. The calibration curves for the six quaternary ammonium disinfectants was linear in the concentration range of 0.1–5.0 ng/mL with correlation coefficient higher than 0.996 0. The limit of detection (LOD) was 0.5 μg/kg and the limit of quantification (LOQ) was 1 μg/kg. The recoveries were 72.8%-102.3% for spiked solid matrix samples, and 71.8%–100.8% for spiked liquid matrix samples with relative standard deviations (RSDs) in the range of 0.25%–3.88% and 0.19%–2.51%, respectively. The proposed method is simple, efficient, rapid, sensitive, and suitable for the qualitative and quantitative analysis of quaternary ammonium disinfectant residues in food for special medical purposes.