Objective The clinical characteristics of 9 cases of neonatal onset of chronic granuloma (CGD) were analyzed to explore the clues of early diagnosis of CGD. Methods The family history, clinical manifestations, auxiliary examination, treatment and prognosis of 9 patients with neonatal-onset CGD were summarized and analyzed. Results All the 9 patients were boys. The median age of onset was 15 days, and the median age of diagnosis was 36 days. At the onset of the disease, there were fever, shortness of breath and difficulty breathing, and 6 cases had coughing. In all patients, the white blood cells measured for the first time ranged from 11.00 ×10⁹/L to 30.51×10⁹/L and were characterized by elevated neutrophils. CRP levels ranged from 37.16 mg/L to 186.30 mg/L. Multiple nodules and mass high density shadows were seen in CT of the lungs. All 9 patients had pulmonary aspergillosis. Respiratory burst test was positive in 2 cases. There were 7 cases of CYBB gene variation and 1 case of NCF1 gene variation. Three patients died, 5 survived and 1 lost follow-up. Conclusions In case of pulmonary aspergillosis infection in neonatal stage, we should be alert to CGD when the imaging changes mainly include multiple pulmonary node shadow and mass high density shadow. The most common variant gene of neonatal CGD is CYBB. The genotype can be frame-shifting, missense, splicing and nonsense mutations. The relationship between genotype and clinical phenotype needs to be further explored.