Metabolic disorders in maternal generation during the late egg-laying period have adverse effects on neonatal development. The study was conducted to clarify the effects of maternal feeding of hawthorn-leaf flavonoid (HF) on the microbial community and intestinal development of chicks. Breeder hens were fed a basic corn-soybean diet, while the treatment groups were supplemented with 30 or 60 mg/kg HF. The offspring chicks were divided into CON, LHF, and HHF groups according to the maternal treatments. Maternal HF supplementation at 60 mg/kg increased the average daily gain and decreased the feed conversion rate of chicks (P < 0.05), but did not affect the average daily feed intake. HF treatments increased the villus height to crypt depth ratio and up-regulated the protein expressions of PCNA, IGF-1R, PI3K and p-mTOR in the jejunum (P < 0.05) of 1-day-old and 14-day-old chicks. Additionally, maternal HF treatment up-regulated the mRNA expression of tight junction transmembrane proteins (occludin) and scaffolding proteins (ZO-1 and ZO-2) in the jejunum of 1-day-old chicks (P < 0.05). Moreover, the maternal effects of HF on ZO-1 expression could last for 14 d (P < 0.05). Interestingly, dietary HF supplementation altered the vertically transmitted microbial community from breeder hens to chicks, especially increased the relative abundance of probiotics (i.e., Clostridium_sensu_stricto_1) in the meconium of chicks (P < 0.05), which may help with early gut microbiota colonization and intestinal development. In summary, dietary HF supplementation for breeder hens altered the bacterial community of neonates and might promote intestinal development of chicks through the IGF-1R/AKT/mTOR signaling pathway.