In this study, two different concentrations of matrix certified reference materials (CRMs) were produced for the accurate measurement of aflatoxin M1(AFM1) in milk powder (GBW(E) 100552, GBW(E) 100553). The raw material was obtained by feeding cows with positive drugs. The homogeneity, stability and characterization of these matrix CRMs were examined by liquid chromatography tandem mass spectrometry with isotope-labeled internal standard method. The certified value for the low concentration of AFM1 in milk powder was 2.45 µg/kg with an expanded uncertainty of 0.43 µg/kg (coverage factor k = 2, at 95% confidence). The certified value for the high concentration of AFM1 in milk powder was 3.45 µg/kg with an expanded uncertainty of 0.49 µg/kg (coverage factor k = 2, at 95% confidence). In addition, the samples were evaluated in detail for homogeneity, long-term stability at − 80 °C for 6 months and short-term stability at 4 °C for 7 days. The results showed that the samples were stable and homogeneous under the above conditions.