A method for the determination of perchlorate and chlorate in bovin milk and infant formula by high performance anion exchange chromatography-tandem mass spectrometry was developed. It was optimized about the protein precipitation reagent and the purification conditions of infant formula. The protein was precipitated by acetonitrile and the supernatant was purified by ion chromatographic pretreatment column. The separation was performed on a Dionex IonPac AS19 high performance anion column with gradient elution using potassium hydroxide eluent at the flow rate of 0.35 mL/min. The injection volume was 50 μL. The column temperature was 30 ℃. The results showed that the perchlorate and chlorate could be separated well under the experimental conditions and showed a good linear relationship with its corresponding quantitative ion peak area in a wide concentration range (R2>0.999). The limits of detection for perchlorate and chlorate were 7 ng/L and 1.7 ng/L， respectively， and the limits of quantification were 20 ng/L and 5 ng/L. The recoveries of milk and infant formula were 88.95%~102.33%， and the RSDs were 1.86%~3.21%. This method has the advantages of simple sample processing， low limit of detection， low limit of quantification， good stability， good repeatability and recovery， and could be widely used in the detection of milk and infant powder.