Using gas chromatography-tandem mass spectrometry (GC-MS), an indirect method was established for the simultaneous detection of 3-chloropropanol esters (3-MCPDE) and glycidyl esters (GE) in infant formula for special medical purposes. The conditions for sample extraction and transesterification/hydrolysis were optimized and stable isotope dilution was used to improve the accuracy and precision of the method. The results showed that the method exhibited good linearity in the range of 0.005–2.000 μg/mL (R2 ≥ 0.999), together with a limit of detection (LOD) of 5 μg/kg and a limit of quantification (LOQ) of 25 μg/kg (both calculated based on the corresponding amount of chloropropanol). The recoveries of the analytes spiked in infant formula for special medical purposes at 25, 125 and 250 μg/kg were 88.5%–104.1%, and the relative standard deviations (RSDs) for six replication determinations were less than 15% (n = 6). The levels of 3-MCPDE and GE in three types of commercial infant formula for special medical purposes were below the maximum limits set by the EU.