The article analyzed the status quo of the new rural cooperative medical system (NRCMS) in Nanjing city. The results of the investigation showed that NRCMS covered the rural population that increased continuously and the financing level rose year by year. It had realized severe illnesses orchestration that was more than other illnesses as principle of the policy, but the funds surplus rate was higher. The hospitalization person distribution was unbalance in the different rank hospitals. The author suggested that the service behavior of the contract medical treatment organization should be normalized, medical practice in hospital should be pursued class by class, township health center should strengthen building up, and reimbursement method and the way of expenses to pay should be actively carried out. NRCMS management information system should be built up and improved.