In the present study, we aimed to evaluate the effects of maternal yeast-based nucleotide (YN) supplementation on the intestinal immune response and barrier function in neonatal pigs, as well as the diarrhoea rate and growth performance in suckling piglets. Sixty-four late-gestation sows were assigned to the following groups: the CON (fed a basal diet) and YN groups (fed a basal diet with 4 g YN/kg diet). The experiment started on d 85 of gestation and ended on d 20 of lactation. Diarrhoea rate and average daily gain of the piglets were recorded, and samples of blood and intestines from neonatal piglets were collected before they consumed colostrum during farrowing. Compared with the CON group, maternal YN supplementation increased the weaning weight of litter and decreased the diarrhoea rate (P < 0.01). In addition, maternal YN supplementation promoted the ileal villus development in the neonates compared with that in the CON group (P < 0.01). Maternal YN supplementation also increased the ileal secretory immunoglobulin A (sIgA) level compared with that in the CON group (P < 0.05). The real-time PCR results showed that maternal dietary YN supplementation increased the jejunal and ileal expression of interleukin (IL)-17, IL-8, IL-1β, IL-10 and tumor necrosis factor (TNF)- α in the neonates compared with that in the CON group (P < 0.05). Overall, maternal nucleotide supplementation improved the villus development and innate immunity of neonatal piglets during late pregnancy. This may be associated with the decrease in diarrhoea and the increase in weaning weight of the litter of suckling piglets.