The article first analyzes the subject of higher education resource allocation, understand the government, market and universities and resource allocation, and then analyzes the internal relationship of higher education resource allocation tools and ontology value orientation, summarizes the direction of higher education resource reform, concluded that the necessity of higher education resource allocation market reform, including adapt to market economy social development demand, effectively solve the contradiction between resource shortage and waste, realize the coordinated development of tool value and ontology value, the pursuit of education fairness. Finally, from the three aspects of market guidance, government control, and university autonomy, explore the market reform path of higher education resource allocation, implement the value orientation, and promote the sustainable development of colleges and universities.