The patient was a 12-year-old boy of Han ethnic group who lived in Xiangyun County, Dali. The patient complained of wet cough on August 2, 2020, and took amoxicillin capsules for 3 days, without relief. Then he was brought to the local clinic and received amoxicilin/Clavulanate potassium, potassium sodium dehydroandroan drographolide succinate for injection and bromhexine hydrochloride for 3 days. The patient was subsequently referred to the Department of Pediatrics of the Xiangyun County People’s Hospital due to fever, shortness of breath and cyanosis on August 11, 2020. The blood routine test showed elevated white blood cells and eosinophils. The chest CT scan showed a large cystic mass with a thick wall in the left lobe of the lung. The patient was misdiagnosis as lung abscess and severe pneumonia, received intravenous vancomycin for 3 days, but also in fever. The patient was admitted to Kunming Children’s Hospital with diagnosed as pneumonia and lung abscess on August 14, 2020. The patient, who was an inhabitant of a rural area, had a history of prolonged exposed to domestic dogs and goats. Laboratory investigations showed marked eosinophilia and positive Echinococcus IgG antibody. The chest CT scan showed infiltration in the lung and a large cystic mass in the left upper lobe of the lung with curvilinear septa within the lesion. The Water-Lily sign was reported. The patient was therefore diagnosed with pulmonary cystic echinococcosis. Removal of cyst in the left upper lobe of the patient’s left lung. The pathological biopsy identified E. granulosus parasite in the lung tissue. The total DNA was extracted from the paraffin-embedded samples of the hydatid cyst, and the molecular analysis was performed. The amplified PCR products were purified and subjected to direct sequencing. The results showed 99.2% sequence identity to the cox2 gene of mitochondrial of E. granulosus. The patient was administrated with albendazole at oral dose of 10 mg/(kg•d), twice a day for 3 months. The body temperature of the patient returned to normal and without cough. A postoperative chest CT scan showed the cavity in the left upper lobe of the lung was significantly reduced and sufficient expansion of the lung in the sixth mouth. Recurrence was not observed for more than 18 months of follow-up.