Arginine plays an important role in preventing intestinal dysfunction and metabolic disorders caused by early weaning stress. However, little is known about how arginine mitigates early weaning stress. This study was conducted to evaluate the effects of weaning stress and dietary arginine supplementation on the metabonome in the serum of piglets using (1)H NMR spectroscopy in conjunction with multivariate data analysis. Thirty castrated male piglets aged 21 d were evenly divided into three groups and fed in three different regimes: sow-fed (SF), weaned with l-alanine supplementation (ALA), and weaned with arginine supplementation (ARG). We found that early weaning stress led to a significantly reduced bodyweight gain (15.6%) and that supplementation with arginine can improve growth rates in piglets by 5.6% (P < 0.05). The early weaning stress was associated with marked alterations in lipid and amino acid metabolisms and perturbations in population and/or activities of gut microorganisms, which were manifested in increased levels of organic acids, amino acids, and acetyl-glycoproteins and reduced levels of choline metabolism and lipoproteins. Dietary supplementation with arginine could partially counteract the changes of metabolites induced by weaning stress, such as lipid and amino acid metabolisms. However, arginine was not able to restore disturbed gut microbiota. These results demonstrate the central role of arginine supplementation in regulating the metabolisms of weaned piglets.