The potential mechanisms about the health risks of endogenous 3-MCPD remain elusive. Here, we researched the influences of 3-MCPD on the metabolic landscape of digested goat infant formulas via integrative UHPLC-Q-Orbitrap HRMS-MS/MS-based peptidomics and metabolomics (%RSDs≤7.35%, LOQ 2.99-58.77μgkg-1). Digested goat infant formulas under 3-MCPD-interference caused metabolic perturbation by down-regulating levels of peptides VGINYWLAHK (5.98-0.72mgkg-1) and HLMCLSWQ (3.25-0.72mgkg-1) pertained to health-promoting bioactive components, and accelerated the down-regulation of non-essential amino acids (AAs, l-tyrosine 0.88-0.39mgkg-1, glutamic acid 8.83-0.88μgkg-1, and d-aspartic acid 2.93-0.43μgkg-1), semi-essential AA (l-arginine 13.06-8.12μgkg-1) and essential AAs (l-phenylalanine 0.49-0.05mgkg-1) that provide nutritional value. Peptidomics and metabolomics interactions elucidated that 3-MCPD altered the stability of α-lactalbumin and d-aspartate oxidase in a dose-dependent manner, and affected the flavor perception of goat infant formulas, leading to a decline of nutritional value of goat infant formulas.