Introduction: Chlamydia psittaci pneumonia is a zoonotic infectious disease caused by Chlamydia psittaci. Its clinical manifestations are nonspecific. Diagnosis of the disease is difficult. In recent years, next-generation sequencing has played an important role in pathogen detection. We report two cases with severe Chlamydia psittaci pneumonia confirmed by next-generation sequencing. Case Study: The first case is that of a 50-year old man who presented with high fever for four days and cough with sputum for two days. The second case is that of a 57-year-old man who was admitted with high fever for one week, dyspnea and cough with sputum for four days. The second man worked at a chicken farm in the last two months. In both cases, the usual laboratory examination for pathogens detection was negative, and the initial anti-infectious therapy had limited effect. The bronchoalveolar lavage fluid of case 1 and the blood and sputum of case 2 were sent for next-generation sequencing which resulted in sequence reads of Chlamydia psittaci. Antibiotics were adjusted according to the diagnosis. Results: The diagnosis of the two cases was confirmed by next-generation sequencing detecting Chlamydia psittaci, and the patients had positive results after treatment. Conclusions: The two cases suggest that next-generation sequencing could be used in early diagnosis of Chlamydia psittaci infection to initiate specific anti-infection therapy in time.