A method for allocate that cost of medical service and calculating the individual benefit of case includes such steps as step 1: carrying out multi-level allocate and cost accounting on the cost of hospital departments, dividing the allocating departments into clinical service departments, medical technology departments, medical auxiliary departments and administrative and logistic departments, dividing the cost of hospital departments into two parts, allocating the cost of hospital departments, and calculating the cost of hospital departments. The multi-level apportionment is a five-level andfour-level apportionment mode for the indirect cost, and the apportionment of the medical service cost is ultimately refined into individual patients; Step 2: Refine the case income structure to include: Revenue from pharmaceuticals (western medicine, traditional Chinese medicine, proprietary Chinese medicine), Consumables income (treatment, surgery, examination), treatment income, surgical income, examination income and other details, matching with the cost-sharing items, income minus cost corresponding statistics of each individual patient's income, thus providing a credible data support for the hospital to carry out targeted income performance evaluation and the decision-making of the doctor group and the department.