This study investigated the effects of different functional oligosaccharides on the growth performance, intestinal barrier function and gut microbiota of weanling piglets. A total of 192 weanling piglets were randomly allocated into 4 dietary groups, which were a control (CON), CON + 0.1% xylo-oligosaccharide (XO), CON + 0.1% isomalto-oligosaccharide (IM) or CON + 0.08% mannan-oligosaccharide (MO) diet. Results showed that the XO and MO groups showed lower diarrhea incidence in weanling piglets compared with the CON group (P < 0.05). Colonic goblet cell numbers and the mRNA expression of mucin-2 (P < 0.05) were greater in all functional oligosaccharide groups. Both the XO and MO groups had a greater concentration of sIgA, IL-10, SOD and GSH-Px and higher antioxidase activity, and the XO group had a lower protein expression of NF-κB in the ilea of piglets (P < 0.05) compared with the CON group. The XO group had a greater concentration of butyrate and an abundance of Bifidobacterium in the ileum (P < 0.05). The MO group had a greater ileal concentration of acetate compared with the additional dietary treatments and greater butyrate compared with the IM and CON groups (P < 0.05). In summary, XO increased the growth of Bifidobacterium, butyrate production and intestinal antioxidant capacity; however, MO promoted the expression of tight junction proteins and the intestinal immune function to reduce piglet diarrhea.