Objective To explore the clinical manifestations, ciliary structure and genetic variation characteristics of primary ciliary dyskinesia (PCD). Methods A retrospective analysis of the clinical data of children diagnosed with primary ciliary dyskinesia (PCD) by bronchoscopic mucosal biopsy electron microscopy or whole exome sequencing (WES) from January 2017 to December 2024 at the hospital. Results A total of 14 children (4 boys and 10 girls) were included, the median age of onset was 6.3 (1.3-7.9) years, and the median age of diagnosis was 8.0 (7.0-10.8) years. The main clinical manifestations included chronic wet cough (14 cases, 100%), rhinosinusitis (12 cases, 85.7%), bronchiectasis and atelectasis (9 cases, 64.3%), situs inversus (3 cases, 21.4%), and chronic otitis media (2 cases, 14.3%). All 14 children presented with bronchoscopic findings of purulent bronchitis (100%), 2 patients were combined with bronchial stenosis, and 1 was combined with bronchial occlusion under bronchoscopy. Nasal exhaled nitric oxide (nNO) was detected in 10 children at least 2 weeks after the acute infection was controlled. nNO was significantly decreased in 8 cases, and nNO was > 77 nL/min in 2 cases. Seven children underwent exome sequencing. Among them, 2 children were negative and 5 were detected with biallelic variations (2 cases of DNAH5 gene variation, 2 cases of CCNO gene variation, and 1 case of DNAH1 gene variation). Conclusions The clinical phenotypes of PCD are mainly chronic cough, sinusitis, and bronchiectasis, with low incidence of situs inversus and neonatal respiratory distress. Some children have nNO levels above the positive threshold and may develop bronchial obstruction. The main gene variations are DNAH5 and CCNO.