The problems in economic operational situation of public hospital are as follows: the structure of income and cost is unreasonable; drug mark-up policy doesn’t decrease drug cost and the growth of medical revenue depends on pricing policies of medical services; the government financial compensation is absent and the working-value compensation to medical personnel is inadequate;hospital developes rapidly in extensive manner and medical expenditure grows rapidly; imperfect medical insurance system constraints the economic operation of hospital. The countermeasures to perfect the economic operational mechanism of public hospital are as follows: the government should pay an important role in raising the proportion of finance compensation and medical compensation, improve pricing police of medical service and guide the medical payments;perfect the coordinating mechanism between medical insurance sector and hospital;reform personnel distribution system;strengthen cost accounting;control the growth rate of health-care expense;strengthen brand building;enhance the core competitiveness.