Antibiotics are commonly overused to reduce weaning stress that leads to economic loss in swine production. As potential substitutes of antibiotics, plant extracts have attracted the attention of researchers. However, one of the plant extracts, tannic acid (TA), has an adverse effect on the growth performance, palatability, and intestinal absorption in weaning piglets when used at a large amount. Thus, this study aimed to investigate the effects of a proper dose of microencapsulated TA on the growth performance, organ and intestinal development, intestinal morphology, intestinal nutrient transporters, and colonic microbiota in weaning piglets. Forty-five Duroc × [Landrace × Yorkshire] (initial body weight = 5.99 ± 0.13 kg, weaned days = 21 d) piglets were randomly divided into five treatment groups (n = 9) and raised in 14 d. The piglets in the control group were raised on a basal diet; the piglets in the antibiotic test group were raised on a basal diet with three antibiotics (375 mg/kg Chlortetracycline 20%, 500 mg/kg Enramycin 4%, 1,500 mg/kg Oxytetracycline calcium 20%); and the other three groups were raised on a basal diet with three doses of microencapsulated TA (TA1, 500 mg/kg; TA2, 1,000 mg/kg; TA3, 1,500 mg/kg). All the piglets were raised in the same environment and given the same amount of nutrients for 2 wk. The results showed that both TA1 and TA2 groups had no adverse effect on the growth performance, organ weight and intestinal growth, and the pH value of gastrointestinal content. TA2 treatment improved the duodenal morphology (P < 0.05), increased the gene expression level of solute carrier family 6, member 19 and solute carrier family 15, member 1 (P < 0.05) in the ileum, and modulated the colonic bacteria composition (P < 0.05), but inhibited the activity of maltase in the ileum (P < 0.05) and the jejunal gene expression level of solute carrier family 5, member 1 (P < 0.05). In conclusion, our study suggests that a dosage between 500 and 1,000 mg/kg of microencapsulated TA is safe to be included in the swine diet and that 1,000 mg/kg of microencapsulated TA has beneficial effects on intestinal morphology, intestinal nutrient transporter, and intestinal microbiota in weaning piglets. These findings provide new insights into suitable alternatives to antibiotics for improving growth performance and colonic microbiota.