Objective To explore the application of next generation sequencing (NGS) in the diagnosis of intractable respiratory diseases in children. Methods A retrospective analysis was performed on the diagnosis of intractable diseases with respiratory symptoms as the main manifestations in the respiratory center of our hospital from 2016 to 2021, and the clinical effectiveness of NGS was further evaluated. Results A total of 97 children underwent NGS testing, all of which had respiratory symptoms as the first or main manifestation. The median age was 1 year and 11 months, and the male to female ratio was 1.4:1 (57/40). Using NGS testing, 31 cases of monogenic disease were diagnosed at a median age of 4 years, and the diagnosis rate was about 32.0%. Among them were 20 cases of primary ciliary dyskinesia. The results of gene detection showed that 18 cases had compound heterozygous mutation, including seven cases of HYDIN, three cases of CCNO, two cases of CCDC40, two cases of DNAH1, one case each of DNAAF3, DNAI2, DNAH11, RSPH4A, homozygous mutation at DNAI2 gene and of hemizygous deletion of PIH1D3 gene. There were four cases of cystic fibrosis, among them three cases had compound heterozygous mutation in CFTR gene and one case had a homozygous mutation of c. 4056G > C in CFTR gene. There were three cases of pulmonary surfactant metabolic disorder, all of them had heterozygous mutations in SFTPC gene. There were two cases of primary immunodeficiency disease, including one case of PI3K δ overactivation syndrome caused by PIK3CD gene mutation and one case of WHIM syndrome caused by CXCR4 gene mutation. There were two cases of neuromuscular diseases including one case of centronuclear myopathy caused by MTM1 gene mutation and one case of progressive spinal muscular atrophy caused by homozygous deletion of SMN1 gene. The clinical manifestations of 31 children with positive gene test included chronic wet cough (n=27), shortness of breath (n=10), recurrent nasal congestion (n=18), runny nose (n=18), external ear pus (n=6), malnutrition (n=11), visceral transposition (n=3) and clubbing finger (n=5). Chest CT revealed bronchiectasis in 14 cases, atelectasis in eight cases and pulmonary interstitial changes in eight cases. The 66 children with negative genetic test were mainly manifested by recurrent respiratory tract infection and chronic cough, with or without bronchiectasis, some children presented with unexplained shortness of breath and respiratory distress, with or without extensive interstitial changes in the lungs. Conclusion Monogenic disease in children with respiratory symptoms as the first or main manifestation has a high degree of clinical and genetic heterogeneity. The application of the next generation sequencing brings new ideas to its diagnosis and treatment and expands people's understanding of the disease spectrum.