Intrauterine growth restriction (IUGR) is not only an underlying factor for stunted postnatal growth and newborn deaths, but also associated with disease prevalence, such as hypertension and diabetes, in both adult humans and animals. To investigate the metabolic status of IUGR, the differences in serum and jejunal tissue metabonome were examined in IUGR and normal weight 21 day old piglets. IUGR piglets had a significantly lower birth weight (785 ± 42 g vs. 1451 ± 124 g), weaned weight (3053 ± 375 g vs. 6489 ± 545 g) and average daily gain (108 ± 16 g vs. 240 ± 21 g) than normal weight piglets (p < 0.05). IUGR piglets also had a shorter villus height and smaller villus height to crypt depth ratio (p < 0.05) in jejunum. An NMR-based metabonomic study found that serum levels of glycoprotein, albumin and threonine were higher in IUGR than in normal weight piglets, while serum levels of HDL, lipids, unsaturated lipids, glycerophosphorylcholine, myo-inositol, citrate, glutamine and tyrosine were lower in IUGR piglets (p < 0.05). In addition, marked changes in jejunal metabolites, including elevated levels of lipids and unsaturated lipids, and decreased levels of valine, alanine, glutamine, glutamate, choline, glycerophosphorylcholine, trimethylamine-N-oxide, scyllo-inositol, lactate, creatine, glucose, galactose, phenylalanine, tyrosine, glutathione, inosine and taurine were observed in IUGR piglets (p < 0.05). These novel findings indicate that IUGR piglets have a distinctive metabolic status compared to normal weight piglets, including changes in lipogenesis, lipid oxidation, energy supply and utilization, amino acid and protein metabolism, and antioxidant ability; these changes could contribute to impaired growth and jejunal function.