Objective To investigate the correlation between changes in intestinal flora and allergic rhinitis (AR) in children.Methods A total of 38 children diagnosed with AR from October 2021 to June 2022 in our department were included as the case group (21 males and 17 females, aged from 5 to 7 years with an average age of 5.85), and 38 normal children were included as the control group (23 males and 15 females, aged from 5 to 7 years, with an average age of 5.80). Stool specimens of the two groups were collected for high-throughput sequencing, and their clinical data were statistically analyzed.Results The Alpha diversity indexes of intestinal flora as Chao1, Observed species,Shannon, Simpson, Faith’s pd and Pielou_e in children with AR were significantly lower than those in the healthy ones. Beta diversity was different between the two groups. There were differences between the two groups on the levels of Actinobacteria and Bacteroidetes, and on the levels of Bacteroides and Bifidobacterium. Body weight (P=0.024), passive smoking (P=0.006), family history of anaphylaxis (P＜0.001), family residence (P=0.017), presence of eczema (P=0.011), use of antibiotics during the neonatal period (P＜0.001), breastfeeding >3 months (P=0.003), caesarean section (P=0.043) may be the influencing factors of AR.Conclusions The diversity of intestinal flora in children with AR is changed compared with that in healthy children. The diversity and stability of intestinal flora ecosystem are decreased, and the abundance of several specific bacterial species is significantly changed. Imbalance of intestinal flora may be an important factor in promoting the development of AR in children.