Esters of 2- and 3-monochloropropane-1,2-diol (MCPD) are vital contaminants of processed edible oils used as foods or food ingredients. The aim of this study was to develop and validatea new method by GC-MS for the simultaneous quantification of 2-MCPD, 3-MCPD in infant milk powder and edible vegetable oils. The developed protocol included fat fraction in infant milk powder and edible vegetable oils samples was extracted and treated with sodium methylate–methanol to cleave the ester bonds of the 2- and 3-MCPD esters, moreover, standard samples of deuterium isotope–labeled 2- and 3-MCPD palmitic acid double esters and stearic acid double esters were used as the internal standards. Furthermore, this method was validated when it was applied to food products, concrete manifestation in its good accuracy (the recovery of MCPD esters ranged from 86% to 114%), high sensitivity (the LOD of 3-MCPD and 2-MCPD esters were 0.025 and 0.020 mg/kg, LOQ were 0.075, 0.060 mg/kg, respectively) and satisfactory repeatability (RSD below 6.8%) for all analytes. In the 150 commercial edible vegetable oils and infant formula milk powder samples, we obtained a preliminary profile of MCPD ester contamination.