Abstract: There are many problems in the specific implementation process of comprehensive budget management in hospitals, of which there are two major problems, the first is how to establish a scientific budget method, which involves statistical problems of medical big data; the second is how to use a computer system to implement and apply the budget system, so that the complex professional calculation process is expressed in a computer interface that is easy for ordinary medical and nursing administrators to understand, and it is convenient for medical and administrative personnel to understand and make the implementation of decision. It mainly expounds the data modeling method of establishing the comprehensive budget management of the hospital from these two aspects to discuss and implement the computer system application system.