Lactose is one of the most commonly used pharmaceutical excipients. Depending on manufactures, the properties of lactose are very different, which could impact the pharmacokinetic behavior of drug products. Therefore, it is very important to trace the origin of pharmaceutical lactose in drug products which is valuable for prescription analysis. In this study, the carbon, hydrogen and oxygen isotope ratios (δ13C, δ2H and δ18O) of thirty-four lactose from seven manufacturers were analyzed by elemental analysis-stable isotope ratio mass spectrometry (EA-IRMS). One-way analysis of variance (ANOVA) and Duncan's test indicated significant differences in isotope ratios of lactose from different origins. To identify the lactose manufacturer, a discrimination model was generated through linear discriminant analysis (LDA). Based on this model, the manufacturers of lactose used in three drug products were successfully identified. Our results suggested that the multidimensional analysis of δ13C, δ2H and δ18O of lactose provided a fast and effective method to trace the lactose manufacturer. In conclusion, this method can be used to analyze the prescription of the drug product quickly, which could speed up the development of generic drug product.