A gas chromatography-tandem mass spectrometry (GC-MS/MS) method for the detection of 3-chloropropanol and glycidyl esters in infant formula milk powder was established, and the content of 3-chloropropanol and glycidyl esters in different commercial infant formula milk powders was determined. Ester contamination and health risk assessment in infant formula milk powder was carried out. 3-Chloropropanol and glycidyl esters in samples were extracted with n-hexane, hydrolyzed, derivatized with phenylboronic acid, detected by GC-MS/MS, and quantified by an internal standard method. The results showed that the total amount of 3-chloropropanol and glycidyl esters was in the range of 0.0400–4.00 μg/mL, and good linearity was observed for 3-chloropropanol esters in the concentration range of 0.0200–2.00 μg/mL with correlation coefficient (R²) greater than 0.999. The limit of detection (LOD) was 10.0 μg/kg, and the limit of quantification (LOQ) was 25.0 μg/kg for both esters. At spiked levels of 25.0, 100 and 300 μg/kg, the average recoveries ranged from 95.0% to 98.1%. The developed method had high accuracy and recovery, and could be used for the detection of 3-chloropropanol and glycidyl esters in infant formula milk powder. In 150 commercial infant formula milk powder samples, the detection rate of 3-chloropropanol esters was 12.7% at levels of ND–52.4 μg/kg with an average of 29.8 μg/kg. The detection rate of glycidyl esters was 6.67% at levels of ND–40.1 μg/kg with an average of 31.9 μg/kg. The average exposure level to 3-chloropropanol esters was 0.33–0.66 μg/(kg·d). Therefore, attention should be paid to the problem of contamination of 3-chloropropanol and glycidyl esters in infant formula milk powder.