Most studies of the evaluation of the new rural cooperative medical insurance system mainly focus on care and health fields, but neglect a more comprehensive index, namely happiness. Under the people-oriented scientific development outlook, the essence of the new rural cooperative medical insurance system is to increase the happiness of farmers through a series of measures such as the reduction in the burden on farmers, the promotion of farmers’ health and transparent & simplified reimbursement procedures. This paper uses the data of CFPS in 2010 and 2012 and CHNS in 2006, 2009 and 2011 to examine the effect of the new rural cooperative medical insurance system on farmers’ happiness. It shows that the implementation effectiveness of the new rural cooperative medical insurance system is not ideal. Further grouping study based on sex, age, income, education and regions indicates that partial effectiveness of the new rural cooperative medical insurance system is also not ideal. It may be due to some problems of the new rural cooperative medical insurance system such as low reimbursement rate, narrow reimbursement scope and fussy reimbursement procedures. Therefore, from an academic perspective this paper supports the necessity of the improvement of the new rural cooperative medical insurance system, that is to say, the improvement of the new rural cooperative medical insurance system focuses on not only the increase in reimbursement rate and scope, but also the simplification of reimbursement procedures and processes and the rise in the transparency of reimbursement rules, so as to comprehensively raise farmers’ satisfaction with the new rural cooperative medical insurance system.