There is a big gap between the amount of fiscal subsidies in the New Rural Cooperative Medical Care System (NRCMCS)and the demand of the farmers, and there is an objective need for the government to raise the subsidies. But as farmers' limited rationality and individual contributions to the earlier and the same proportion of growth and financial assistance, a paradox was form ed that farmers need the medical subsidies from the government but at the same time, they do not want to pay more.And the paradox becomes more serious because of the supply deficiency in policy.Thus, an optimized allocation is needed for the fiscal subsidies in the NRCMCS.There are many feasible ways in allocating the subsidies, such as designing flexible ensuring modes, adjiusting the increase range between the farmers' payment and govern ment subsidies, raising the proportion of farmers' medical reimbursement, etc.