Objective: To investigate the impact of New Rural Cooperative Medical System (NCMS)on rural resident’s medical burden. Methods: It investigates the survey data from the China Health and Nutrition Survey and employing difference-in-difference method based on the fixed effect model. Results: NCMS increases rural resident’s actual reimbursement rate, release the high health medical expenditure, but has limit impact on medical expenditure. The low-income group has greater risk on high medical expenditure. Conclusion: It is needed to improve the level of NCMS policy implementation; strengthen the supervision of designated medical institutions and increase policy support for low-income rural residents.