Objective To discuss the characteristics of intestinal flora in rat allergic rhinitis (AR) with deficiency syndrome of lung and spleen Qi.Conclusion The modeling of allergic rhinitis lung and spleen Qi deficiency syndrome had statistical significance on the formation of intestinal flora: the diversity of intestinal flora of allergic rhinitis lung and spleen Qi deficiency model rats decreased significantly. From the perspective of community structure, AR significantly drove the dynamic changes of the whole rat microbial community and had statistical significance. The Biomarker explored in this study can be used for the early auxiliary diagnosis of AR and lung and spleen Qi deficiency syndrome.