Objective: To analyze the operating status of new rural cooperative medical system(NCMS) in Guizhou, so as to provide references for medical insurance policy making and promoting the safety of medical insurance for urban and rural residents. Methods: Getting 2006-2016 NCMS data of 54 counties (cities, districts) of Guizhou from the NCMS management. Then using SPSS 22.0 software to analyze data from the dimensions of fundraising, expenditure, balance, hospitalization expenses, and farmers' benefit. Results: From 2006 to 2016, the NCMS participation rate and financing level of sample counties in Guizhou increased year by year. The average hospitalization expenses and the actual hospital compensation ratio at all levels of medical institutions increased. The proportion of funds flowing out of the county increased significantly. There are large fluctuations in the balance of the year. In most years the accumulated fund balance rate exceeded 25%. Conclusion: The coverage of NCMS in Guizhou has been expanded. The scale of fundraising has been increased year by year. The mechanism of fund expenditure is imperfect. The use of hospital funds needs to be further regulated. The overall fund balance is sufficient. But there are still some counties had negative balance in the year. And the lack of cost control by NCMS has weakened the farmers' benefit.