BackgroundIntestinal inflammation has become a threatening concern in chicken production worldwide and is closely associated with Th17/Treg cell imbalance. Several studies described that gut microbiota is significantly implicated in chicken growth by modulating intestinal immune homeostasis and immune cell differentiation. Whether reshaping gut microbiota by fecal microbiota transplantation (FMT) could improve chicken growth by balancing Th17/Treg cells is an interesting question.ResultsHere, the chickens with significantly different body weight from three different breeds (Turpan cockfighting × White Leghorn chickens, white feather chickens, and yellow feather chickens) were used to compare Th17 and Treg cells. qPCR and IHC staining results indicated that Th17 cell-associated transcriptional factorsStat3androrγtand cytokinesIL-6,IL-17A, andIL-21were significantly (P< 0.05) higher in the jejunum of low body weight chickens, while Treg cell-associated transcriptional factorfoxp3and cytokinesTGF-βandIL-10were significantly (P< 0.05) lower in the jejunum of low body weight chickens, indicating imbalanced Th17/Treg cells were closely related to chicken growth performance. Transferring fecal microbiota from the healthy donor with better growth performance and abundantLactobacillusin feces to 1-day-old chicks markedly increased growth performance (P< 0.001), significantly decreased Th17 cell-associated transcriptional factors and cytokines, and increased Treg cell-associated transcriptional factors and cytokines in the jejunum (P< 0.05). Furthermore, FMT increased the abundance ofLactobacillus(FMT vs Con; 84.98% vs 66.94%). Besides, the metabolites of tryptophan including serotonin, indole, and 5-methoxyindoleacetate were increased as well, which activated their receptor aryl-hydrocarbon-receptor (AhR) and expressed moreCYP1A2andIL-22to maintain Th17/Treg cell balance and immune homeostasis.ConclusionThese findings suggested that imbalanced Th17/Treg cells decreased chicken growth performance, while FMT-reshaped gut microbiota, i.e., higherLactobacilli, increased chicken growth performance by balancing Th17/Treg cells.Video AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s40168-023-01569-z.