Abstract: Objective To study the nasopharynx microbiome community characteristics of young infants with cough, and the connection with several clinical features. Methods From 2015 to 2017, 72 young infants who had cough were enrolled. Information of gender, age, delivery mode, feeding practices, RSV as well as B.pertussis testing results were collected. Twenty-four cases were positive in B.pertussis culture, while 48 cases were negative. After extracting the genome DNA, the region of V3-V4 was amplified and sequenced. Results The nasopharynx microbiomes of 72 young infants were dominated by five distinct community pneumotypes (C1-C5). The 22 of 24 B.pertussis culture positive cases were detected with Bordetella 16S rDNA, while 34 of 48 negative cases were detected with Bordetella 16S rDNA, with a relative abundance of 0.003%-0.280%. The average relative abundance of B.pertussis in Bordetella culture positive cases (28.38%) was significantly higher than negative cases (0.03%). Besides, the average relative abundance of Staphylococcus and Bordetella in RSV positive cases was significantly lower than negative cases. Conclusion Except for Bordelella, the nasopharynx microbiomes of 72 young infants are resembled previous finding. Culture probably may not work owing to a low abundance of bacteria. RSV can significantly influence the the nasopharynx microbiome community characteristics of young infants with cough.