Objective　To investigate clinical features, diagnosis, and treatment of refractory Mycoplasma pneumoniae pneumonia (MPP) combined with thrombosis. Methods One case with refractory MPP associated with thrombosis was retrospectively analyzed with literature review. Results The patient presented with respiratory symptom at the onset, while melosalgia and decreased respiratory sound in left lung were occurred during anti-infection therapy. Thereafter, thrombosis of lower extremity veins and pulmonary embolism were confirmed by a series of examinations. Serum anti-phospholipid antibody was positive. Finally, the patient was treated with a combination of anticoagulation and immunosuppressive therapies. Conclusions The mechanism of refractory MPP combined with thrombosis may be associated with excessive inflammatory response and endothelial cells injury. The thrombosis complication should be suspected in patient of Mycoplasma pneumonia infection with positive anti-phospholipid antibody and low concentration of protein C and immunosuppressive therapy should be implemented promptly.