To explore the clinical manifestations, diagnosis and treatment of pulmonary thromboembolism associated with protein C (PC)/protein S (PS) deficiency. Two male patients 29 and 26 years old diagnosed with PC deficiency and/or PS deficiency were retrospectively analyzed and related literatures were reviewed. The most common symptoms were pain in the lower limbs with chest pain or decreased vision. Color dopper flow imaging (CDFI) showed lower deep venous phlebothrombosis. Multislice CT angiography (CTA) revealed pulmonary embolism. The level of serum homocysteine (HCY) increased and the level of plasma PC/PS content decreased to PC 57.4%, and PS 28.9% in patient 1, while PS 33.4% in patient 2. Poor routine anticoagulant response was observed. After the diagnosis of PC/PS deficiency, vitamin B6 and B12 anticoagulant therapy was added, and the symptoms in the patients improved significantly. Congenital thrombophilia should be taken into consideration for young patients with lower deep venous thrombosis and pulmonary embolism which occur recurrently without obvious predisposing causes before 40. Plasma PC/PS concentrations or activity help a lot in the diagnosis and treatment.