Tropheryma whipplei (TW) is a kind of Gram-positive bacterium, which belongs to fastidious bacteria and is often difficult to be diagnosed clinically. Whipple's disease is a chronic multi-system infectious disease caused by TW, the common target organs are gastrointestinal tract and joint, pulmonary involvement is rare. This paper reports that the clinical manifestations of the patient are fever, cough and dyspnea, CT finding shows bilateral lungs diffuse ground glass shadow. Metagenomic sequencing of bronchoalveolar lavage fluid shows mixed infection of TW and Candida tropicalis infection. The patient's condition is improved after treated with meropenem, compound sulfamethoxazole, and fluconazole. This paper reports a case of TW pneumonia and reviews the literatures, so as to improve the clinical understanding of TW infection, achieve early diagnosis and treatment.