Background: Recently, new oral anticoagulants (NOACs) have been included in guidelines for the treatment of cancer-associated thrombosis (CAT) to be extended to suitable cancer patients. The purpose of this study was to compare the cost-effectiveness of using NOACs and low molecular weight heparins(LMWHs) for treating CAT from the perspective of the Chinese healthcare system. Methods: A Markov model was constructed to estimate the cost-effectiveness of the two strategies with a 6-month and 5-year time horizon. Input parameters were either sourced from the clinical trial, published literature. The primary outcome of the model was reported as incremental cost-effectiveness ratios (ICERs). Sensitivity analyses were performed to test model uncertainty. Results: The 6-month cost of NOACs was $ 654.65 with 0.40 QALYs while the 6-month cost of LMWHs was $ 1719.31 with 0.37 QALYs. Similarly, treatment with NOACs had a lower cost ($ 657.85 vs. $ 1716.56) and more health benefits (0.40 QALY vs. 0.37 QALY) than treatment with LMWHs in a subgroup of patients with gastrointestinal malignancy. We found treatment with NOACs would result in a large reduction in cost($ 1447.22 vs. $ 3374.70) but a small reduction in QALYs (3.07 QALY vs. 3.09 QALY) compared with LMWHs over a 5-year time frame, resulting in an ICER of $ 112895.50/QALY. Sensitivity analysis confirmed the robustness of the results. Conclusion: As compared to LMWHs, NOACs can be a cost-saving anticoagulant choice for the treatment of CAT in the general oncology population and gastrointestinal malignancy population.Classification codes: I.