Objective: Investigate and evaluate the operation and operating efficiency of the new rural cooperative medical scheme(NRCMS) fund in 36 counties of Yunnan Province from 2006 to 2016.Methods: The data of the NRCMS participation in 36 counties from 2006 to 2016 were obtained with the stratified sampling method. SPSS22.0 software was used to summary, arrange, and describe data. Data envelopment analysis（DEA）was used to assess the efficiency of fund operation in each year. Results: From 2006 to 2016, The coverage rate in Yunnan province for the NRCMS has increased yearly. Overall fund balances fluctuate greatly, the comprehensive efficiency and pure technical efficiency of the NRCMS fund are relatively low. And the scale efficiency of NRCMS was relatively high. The overall efficiency is mainly influenced by the purely technical efficiency and efficiency. Conclusion: The NRCMS in Yunnan performed well from 2006 to 2016. The participation rate and funding level increased yearly. The balance of fund tends to be stable. The comprehensive efficiency of NRCMS is mainly influenced by pure technical efficiency. There is a waste of investment in fund operating, still need to further improve the level of fund management.