Aims: Primary Ciliary Dyskinesia (PCD) is a condition associated with Chronic Rhinosinusitis with Nasal Polyps (CRSwNP). The aim of this research was to examine the impact of carrying PCD gene mutations on susceptibility to CRSwNP in children and to to learn more about the hub genes that influence its pathophysiology. Methodology: Whole Exome Sequencing (WES) was performed on the peripheral blood of 48 CRSwNP children and 104 healthy controls to identify PCD gene mutations and compare them with the population database. Transcriptome sequencing was performed on 38 nasal polyp tissues and 5 normal mucosal tissues to identify differentially expressed genes (DEGs). Joint analysis of WES and transcriptome data was conducted to examine hub PCD-associated genes in the development of CRSwNP. Results: 41 individuals (85.42%) in the CRSwNP reported PCD-related gene mutations. Additionally, 37 (35.57%) people are in the control group. In CRSwNP, 120 mutation sites were found in 37 PCD-associated mutant genes. In descending order of proportion, DNAH9, DNAH11, STK36, HYDIN, and DNAH5 were the top five genes with the largest percentage. The detection of 55 sites was substantially higher than that of the population database at the cutoff values of MAF <0.05 and CADD >15. DNAH9, DNAI2 and ODAD4 had significantly higher detection rates and were risk factors for CRSwNP compared to controls (P<0.05, OR>2). Transcriptome sequencing revealed 4456 DEGs in total. Enrichment analysis showed that cilia-related biological processes, molecular functions and cellular components were significantly enriched. Joint research revealed that DNAH9, DNAI2, and ODAD4 were identified differentially expressed at the gene and transcript levels. Conclusion: In children, the carriage of PCD mutant genes may enhance the susceptibility to CRSwNP. Cilia-associated structural and functional abnormalities play an important role in the development of CRSwNP in children, with DNAH9, DNAI2 and ODAD4 being the hub genes.