The mechanism of allergic rhinitis (AR) remains unclear. Most researchers believe that AR is the result of a combination of environmental and genetic factors. Sublingual immunotherapy (SLIT) is a treatment that can change the natural course of AR through immunomodulatory mechanism and maintain efficacy after the treatment. Nasal cavity is the main site where AR patients contact with external allergens, produce inflammatory reactions and nasal symptoms. Therefore, in this study, we investigate the nasal microbiome in AR patients, and the changes after SLIT. In this cross-sectional study, nasal swabs for microbiome analysis were collected from 3 groups: SLIT-naïve AR patients (AR group), AR patients undergoing SLIT treatment over 2 years (SLIT group) and a control group (CG). The characteristics of nasal microbiome of each groups were produced by 16s-rDNA sequencing technology. The Simpson index of AR group was significantly higher than that of CG and SLIT groups, but not different between SLIT group and CG group. The abundance of Bacteroidete and Firmicutes remarkably increased in the AR group, but Bacteroidete reduced to CG level after SLIT. AR patients have different nasal microbiome composition, but we do not know how it happened and whether the AR condition affected nasal microbiome composition or nasal microbiome affected AR.