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Background Characteristics of airway microbiota might influence asthma status or asthma phenotype. Identifying the airway microbiome can help to investigate its role in the development of asthma phenotypes or small airway function. Methods Bacterial microbiota profiles were analyzed in induced sputum from 31 asthma patients and 12 healthy individuals from Beijing, China. Associations between small airway function and airway microbiomes were examined. Results Composition of sputum microbiota significantly changed with small airway function in asthma patients. Two microbiome-driven clusters were identified and characterized by small airway function and taxa that had linear relationship with small airway functions were identified. Conclusions Our findings confirm that airway microbiota was associated with small airway function in asthma patients.