Background: With the development of sequencing technologies, it has been found that there are microbes similar to those in the upper respiratory tract present in the healthy human lower respiratory tract (LRT), including the lungs and bronchus. Thus, to study the LRT microbiome and evaluate the relationship between this microbiome and allergic respiratory diseases in children, we enrolled 68 children who visited the respiratory department and underwent bronchoscopy from January 2018 to December 2018 in the affiliated hospital of the Capital Institute of Pediatrics. Methods: Using the total IgE (TIgE) values, children were divided into two groups: one group had 34 patients with allergy (allergy sensitivity, AS); the second group had 34 patients with no allergy (no allergy sensitivity, NAS). Nucleic acid was extracted from samples of bronchoalveolar lavage fluid (BALF) taken during bronchoscopy treatment and the 16S rDNA gene was sequenced and analysed. Results: The results showed that Haemophilus, Moraxella, Streptococcus, Prevotella, Neisseria, and Rothia were detected in all patients. There was a statistically significant difference in the composition and distribution of microbiota between the AS and NAS groups (p < 0.01). Compared with children in the AS group, the LRT of those belonging to the NAS group were enriched with Streptococcus, Lactobacillus, and Anoxybacillus. However, the level of Bacteroidetes in the AS group was significantly higher. Analysis of the correlation of clinical indices and microbiome showed that TIgE was positively correlated with Bacteroidetes and negatively correlated with Streptococcus. In addition, absolute lymphocyte count showed a relationship with Streptococcus, and the absolute neutrophil count or percentage of neutrophils showed a relationship with Cardiobacterium.Conclusions: The respiratory tract microbiome functioned similarly to the intestinal microbiome. That is, the decrease in microbial diversity and the change in composition could lead to an increase in allergic symptoms. The colonised microbiota of the LRT in children, especially that of Bacteriodetes and Streptococcus, showed a certain correlation with early respiratory allergic diseases. Trial registration number is ISRCTN18302701, and date of registration is 06/10/2020.