Objective　To investigate the etiology, clinical manifestations, etiological diagnosis and treatment of pneumocystis pneumonia. Methods　The clinical data of a child with pneumocystis pneumonia were retrospectively analyzed. Results　A male infant, aged 2 months and 20 days, presented with chronic cough, shortness of breath, irritability, and hypoxemia. Pulmonary imaging showed diffuse infiltration of both lungs. The metagenomic next-generation sequencing of bronchoalveolar lavage fluid by bronchoscope confirmed pneumocystis infection. Clinical symptoms of the patient disappeared and exudation of lung CT absorbed after treatment with trimethoprim-sulfamethoxazole. Conclusion　Infants should be alerted to pneumocystis pneumonia when having recurrent cough, shortness of breath, hypoxemia and diffuse infiltration in both lungs. Metagenomic next-generation sequencing with bronchoscopic alveolar lavage fluid is a better method for pathogenic diagnosis of pneumocystis pneumonia.