This study was conducted to compare the effects of Eucommia ulmoides leaves (EL) in different forms (EL extract, fermented EL, and EL powder) with antibiotics on growth performance, intestinal morphology, and the microbiota composition and diversity of weanling piglets. Compared to the control group, the antibiotics and EL extract significantly increased the average daily gain and decreased the feed: gain ratio as well as the diarrhea rate (P < 0.05). The EL extract significantly decreased the crypt depth and increased the ratio of villus height to crypt depth (P < 0.05), while the fermented EL group did the opposite (P < 0.05). The crypt depth in the antibiotics group was of similar value to the EL extract group, and was lower than the fermented EL and EL powder groups (P < 0.05). Compared to the control and antibiotics groups, the jejunul claudin-3 mRNA expression and the concentrations of total VFA, Chao 1, and ACE were significantly augmented in the EL extract group of piglets (P < 0.05). The EL extract groups also showed elevated Shannon (P < 0.05) and Simpson (P = 0.07) values relative to the control and antibiotics groups. At the phylum level, the EL extract group exhibited a reduced abundance of Bacteroidetes and an enhanced abundance of Firmicutes. At the genus level, the abundance of Prevotella was augmented in the EL extract group. Moreover, compared with the antibiotic group, the acetate concentration was enhanced in the EL extract and fermented EL groups. Overall, dietary supplementation with the EL extract, but not the fermented EL or EL powder, improved growth performance, jejunul morphology and function, as well as changed colonic microbial composition and diversity, which might be an alternative to confer protection against weanling stress in weanling piglets.