The novel oral anticoagulants(NOACs) including apixaban, dabigatran and rivaroxaban have been widely applied to anticoagulation treatment for non-valvular atrial fibrillation(NVAF). The objective of this study was to evaluate the cost effectiveness of apixaban, dabigatran and rivaroxaban for stroke prevention in patients with NVAF in China. A previously published Markov model was adapted to estimate the costs and quality-adjusted life-years (QALYs) of the three NOACs for patients with NVAF from the perspective of health care system. The model included the following health states: NVAF, ischemic stroke (mild, moderate, severe), hemorrhagic stroke (mild, moderate, severe), systemic embolism, myocardial infarction, NVAF subsequent aspirin and death. The time horizon was lifetime and the cycle length was 6 weeks. In the absence of head-to-head evidence, transition probabilities were derived from indirect comparison analyses based on the ARISTOTLE,RE-LY and ROCKET-AF clinical trials. Published health state utilities were used. Only direct medical costs were considered, obtained from published research on Chinese population. Both costs and outcomes were discounted at 3%. Deterministic sensitivity analysis and probabilistic sensitivity analysis were conducted. The lifetime costs for dabigatran(110mg BID), rivaroxaban(20mg QD), dabigatran(150mg BID) and apixaban(5mg BID) were ¥63,489, ¥76,697, ¥78,078 ,and ¥293,871, while the quality-adjusted life-years were 7.00 QALYs, 7.18 QALYs, 7.07 QALYs and 7.23 QALYs, respectively. Dabigatran(150mg) was dominated by rivaroxaban because of higher cost and lower QALY. The incremental cost-effectiveness ratio of rivaroxaban and apixaban compared with dabigatran(110mg) were ¥71,755/QALY and ¥1012,003/QALY respectively. At a willingness-to-pay threshold of ¥178,980(3 times of China per capita GDP in 2017) per QALY, rivaroxaban was cost-effective. Sensitivity analyses indicated that results were robust. Based on the results of this research, rivaroxaban can be a cost-effective option compared with other NOACs for stroke prevention in patients with NVAF in China.