Deoxynivalenol (DON) causes various toxic effects in human and animals. However, our previous studies have shown that composite antimicrobial peptides (CAP) can have a protective effect in piglets challenged with DON. This study was conducted to evaluate the effect of the CAP GLAM 180# on the metabolism of piglets challenged with DON using a nuclear magnetic resonance (NMR)-based metabolomics approach. A total of 28 individually housed piglets (Duroc × Landrace × Large Yorkshire) weaned at 28 d of age were randomly assigned into 4 treatment groups (7 pigs/treatment) based on a 2 × 2 factorial arrangement that were fed, respectively, a basal diet (NC), basal diet + 0.4% CAP (basal + CAP), basal diet + 4 mg/kg DON (basal + DON), and basal diet + 4 mg/kg DON + 0.4% CAP (DON + CAP). A 7-d adaptation period was followed by 30 d of treatment. Blood samples were then collected for metabolite analysis by proton NMR (H-NMR) spectroscopy and liquid chromatography tandem mass spectrometry (LC-MS/MS). The combined results of H-NMR spectroscopy and LC-MS/MS showed that DON increased ( < 0.05) the serum concentrations of low-density lipoprotein, glycoprotein, urea, trimethylamine-N-oxide (TMAO), and lactate as well as those of almost all essential AA and some nonessential AA but decreased the concentrations of high-density lipoprotein (HDL), unsaturated lipids, citrate, choline, and fumarate compared with those in NC treatment ( < 0.05). There was a significant interaction effect ( < 0.05) of supplementation with DON and CAP on some metabolites showed that the serum concentrations of HDL, unsaturated lipids, Pro, citrate, and fumarate were greater ( < 0.05) whereas those of glycoprotein, urea, TMAO, Gly, and lactate were lower in the DON + CAP treatment compared with those in the basal + DON treatment ( < 0.05). These findings indicated that DON causes disturbances in AA, lipid, and energy metabolism and that CAP could partially attenuate the above metabolic disturbances induced by DON.