Pulmonary embolism (PE) is a serious condition associated with high mortality and an annual incidence around 0.1% among hospitalized patients in China. Compared with standard of care (SOC), combined low molecular weight heparin (LMWH) and vitamin K antagonist (VKA), the direct oral anticoagulant rivaroxaban is easier to use without monitoring and lower bleeding risk. Since there is limited economic evaluation of rivaroxaban among Chinese people, the aim was to estimate the cost-effectiveness of rivaroxaban compared with combined LMWH/VKA form a perspective of the third payer in China. A Markov model was constructed using data derived from EINSTEIN PE studies of rivaroxaban, China health insurance database and other published literature. Main outcomes were total costs, quality-adjusted life years (QALYs) and incremental cost-effectiveness ratios (ICERs). The QALYs and direct medical costs were reported over a 5-year horizon. An annual discount rate with 5% was adopted for costs and outcomes. One-way and probabilistic sensitivity analyses were performed to test uncertainty concerning the model parameters. Rivaroxaban therapy had more QALYs (4.015 vs 4.010) and lower total costs (CNY 40,444 vs. CNY 41,916) compared with LWMH/VKA, which demonstrated it as a cost-saving treatment strategy. The result was most sensitive to the cost per day of hospitalization avoided and length of hospitalization in PE patients on LMWH/VKA. In addition, geometric mean ratio of length of hospitalization of rivaroxaban vs. LMWH and cost of rivaroxaban (per day) were other important variables. At a willingness-to-pay threshold of ¥161,940/QALY(2016), the likelihood of rivaroxaban being cost-effective was 91.3%. In conclusion, rivaroxaban therapy resulted in cost-saving compared with LMWH/VKA for anticoagulation treatment of PE patients in China.