Abstract: With the deepening reform of higher education and the accounting system in colleges and universities, in order to save costs, improve the economic and social benefits of funds, at last realize the sustainable development of colleges and universities. Thus it is necessary to apply comprehensive budget management system in colleges and universities. In thinking of existing problems in the budget management of colleges and universities, a comprehensive budget management system will be built, which includes the target system, organization system, workflow system, working-out system, implementation system, monitoring system and evaluation system. Finally, by the way of comprehensive budget management system, the strategic goal of “double first-class” in colleges and universities will be realized in a short period of time.