Pulmonary artery sarcoma (PAS) is a rare and aggressive mesenchymal tumor that often mimics thromboembolic disease. Due to its rare and fatal nature, patients are often underdiagnosed or misdiagnosed. There is still no consensus regarding the diagnosis and treatment of PAS. We present a case of a 63 year old male misdiagnosed with pulmonary thromboembolism who received anticoagulant therapy. 18FDG positron emission tomography (PET) integrated with computed tomography (PET/CT) and subsequent surgery led to the final diagnosis of PAS. Whole exome sequencing of the tissue identified the genetic alterations profile of PAS: copy number variation (CNV) of KIT and mutations of TP53, PIK3CA, IL7R and ATR. Treated with chemotherapy followed by anlotinib, the patient's survival time was 8 months after firm diagnosis. To our knowledge, anlotinib used as a treatment for PAS has not been reported.