Objective　To summarize the clinical characteristics of primary ciliary dyskinesia (PCD) caused by a novel compound heterozygous mutation in HYDIN gene, and to explore the relationship between mutant genotype and phenotype. Method The clinical data of PCD caused by compound heterozygous mutation in HYDIN gene in a child were retrospectively analyzed. The literature at home and abroad was retrieved by using the key words "primary ciliary dyskinesia HYDIN gene" and "primary ciliary dyskinesia HYDIN". Results　A 3-year- and 1-month-old girl started wet cough and sneezing at the age of 1 year, and it was ineffective to treat with repeated antibiotics and anti-asthma. Lung CT scan showed pulmonary atelectasis in the middle lobe of the right lung. Purulent nasal discharge could be seen through the nasepharyngoscope. Many purulent secretions in the bronchi could be seen under bronchofiberscope. Abnormal microtubule structure of cilia 9+2 was observed under electron microscopy, and a few cilia showed "9+0" and "9+3" structures. Second-generation sequencing confirmed a novel compound heterozygous mutation (c.7963G>T+c.1123 C>T) in HYDIN gene which originated from her parents respectively. There were no reports of this compound heterozygous mutation in literature and databases. Conclusion　C.7963G>T+c.1123 C>T is a novel compound heterozygous mutation in HYDIN gene which may cause PCD in children, and the symptoms are related to the genotype.