Asthma is the common respiratory disorder in children, which is associated with abnormal gut microbiota. Fecal microbiota transplantation (FMT) has successfully ameliorated the symptoms of several diseases and restored the balance of gut microbiota. However, there are few researches about the role of FMT in asthma. This study aimed at exploring whether FMT can alleviate allergic airway inflammation in neonatal mice and elucidating the probable underlying mechanism. A neonatal mouse model of ovalbumin (OVA)-induced allergic asthma was established and transplanted with fecal filtrates. Our results manifested that FMT could protect against the allergic airway inflammation through enhancing mesenteric CD11c + CD103 + DCs and accumulating mucosal Helios + Tregs. Besides, the programmed cell death protein 1/programmed cell death protein 1 ligand (PD-1/PD-L1) signal pathway was inhibited after FMT intervention. Furthermore, this beneficial role of FMT was also associated with the rebalanced gut microbiota, such as Akkermansia. Thus, our findings indicated that FMT intervention could exert a therapeutic effect in a neonatal mouse model of OVA-induced allergic airway inflammation through its remodeling on gut microbiota and regulation of Treg homeostasis via the PD-1/PD-L1 axis, which might be used as an alternative therapy for allergic asthma.