Intrauterine growth retardation (IUGR) delays the gut development of neonates, but effective treatment strategies are still limited. This study used newborn piglets as a model to evaluate the protective effect of polydatin (PD) against IUGR-induced intestinal injury. In total, 36 IUGR piglets and an equal number of normal birth weight (NBW) littermates were fed either a basal diet or a PD-supplemented diet from 21 to 35 days of age. Compared with NBW, IUGR induced jejunal damage and barrier dysfunction of piglets, as indicated by observable bacterial translocation, enhanced apoptosis, oxidative and immunological damage, and mitochondrial dysfunction. PD treatment decreased bacterial translocation and inhibited the IUGR-induced increases in circulating diamine oxidase activity (
P
=
0.039
) and D-lactate content (
P
=
0.004
). The apoptotic rate (
P
=
0.024
) was reduced by 35.2% in the PD-treated piglets, along with increases in villus height (
P
=
0.033
) and in ratio of villus height to crypt depth (
P
=
0.049
). PD treatment promoted superoxide dismutase (
P
=
0.026
) and glutathione S-transferase activities (
P
=
0.006
) and reduced malondialdehyde (
P
=
0.015
) and 8-hydroxy-2
′
-deoxyguanosine accumulation (
P
=
0.034
) in the jejunum. The PD-treated IUGR piglets showed decreased jejunal myeloperoxidase activity (
P
=
0.029
) and tumor necrosis factor alpha content (
P
=
0.035
) than those received a basal diet. PD stimulated nuclear sirtuin 1 (
P
=
0.028
) and mitochondrial citrate synthase activities (
P
=
0.020
) and facilitated adenosine triphosphate production (
P
=
0.009
) in the jejunum of piglets. Furthermore, PD reversed the IUGR-induced declines in mitochondrial DNA content (
P
=
0.048
), the phosphorylation of adenosine monophosphate-activated protein kinase alpha (
P
=
0.027
), and proliferation-activated receptor gamma coactivator 1 alpha expression (
P
=
0.033
). Altogether, the results indicate that PD may improve jejunal integrity, mitigate mucosal oxidative and immunological damage, and facilitate mitochondrial function in IUGR piglets.