Abstract: Fingerprints of common infant formula milk powder (FPⅠ) and of functional infant milk powder (FPⅡ) were obtained by HPLC-Q-TOF-MS. Differences between FPⅠ and FPⅡ were found by the correction model of principle component analysis (PCA). The potential biomarkers were selected by the t-test and the probable proteinic origins were deduced by the data-processing software. Reliability of the biomarkers was verified by applying the hyphenation of LC and MS. As shown by the results, 14 potential biomarkers were found in the functional infant milk powder, with their probable proteinic origins of αS1-casein, αS2-casein and β-casein. Thence, the presence of hydrolyzed protein in functional infant milk powder was deduced, and the presence of these biomarkers was an effective basis to differentiate the functional infant milk powder from the common infant for mula milk powder.