This survey study was conducted to understand the effect of the New Cooperative Medical Scheme (NCMS) on farmers’ medical expenses through comparing the information from five investigations and to obtain a scientific basis for a more applicable NCMS. The survey was carried out through interviewing farmers in their homes. The multi-phase stratified cluster random sampling was adopted to select 3 counties from all 92 counties of the Jiangxi province, 9 townships from the 3 selected counties, 27 villages from the selected 9 townships, and 60 families from each village between 2006 and 2014, and a longitudinal comparative analysis was conducted. The numbers of households/overall sample for the five years were 1924/8082, 1879/8015, 1885/7506, 1890/7857, and 1896/7811, respectively. We collected family members’ social demographic characteristics, health resources, and peoples’ health and medical expenses and reimbursement of each family member. The adjusted hospitalization expenses per capita of township hospitals and county hospitals were totally on a rising trend. However, the costs of tertiary hospitals were on a decreasing tendency. In addition, the expenses for county hospitalization per admission were on an upward trend in general. Furthermore, the total hospitalization expenses and reimbursement per capita (the insurance paid out for the hospitalization expenses) were also all on an upward trend. The proportion of reimbursement also had a tendency of increasing from 24.41% in 2006 to 41.34% in 2014. The costs paid from farmers’ pockets were fluctuated, but in general all lower than the costs in 2006. Furthermore, the percentage of hospitalization expenses from farmers’ annual incomes gradually decreased each year from 56.38% in 2006 to 26.58% in 2014. NCMS program has had an obvious impact on the hospitalization expenses in the Jiangxi rural area. It reduced the hospitalization expenses of the tertiary hospitals significantly. In addition, the program has also encouraged farmers to get more health care. However, there are still some shortages associated with present construction of the NCMS. Hence, there is a need for local government to continue to take effective countermeasures to control the rising trend of hospitalization expense.