Objective To explore the pathogenesis and diagnosis of chronic granulomatous disease. Methods Clinical features and laboratory examination results of a child with chronic granulomatous disease were retrospectively analyzed. Genome DNA was extracted from peripheral blood of the child and his parents. The high-throughput sequencing was performed by Illumina sequencing platform, using the Agilent SureSelect exome capture method. Results The child had recurrent infections along with liver enlargement and dysfunction. The anti-infection and symptomatic treatment were unsatisfactory. Gene sequencing analysis revealed a homozygous point mutation (c.7C > T, p.Gln3*) in CYBA gene. His mother had the same heterozygous mutation in this locus, and his father had a large fragment heterozygous deletions. No other candidate gene mutations were identified. Conclusions The diagnosis of chronic granulomatous disease is confirmed in this child. It is caused by CYBA gene mutation.