Abstract:Regional higher education is the intellectual base and the innovative source which support the regional economic and social development, higher education integration is the key elements of promoting regional innovation. The study analyze the main problems of regional higher education from the perspective of regional innovation system theory, it is found that, there are three main factors restrict the regional innovation of the school level division, the school body dislocation , the isomorphism of school structure, the integration of Specialist, undergraduate, master, doctorate can realize the complementarities of the university function and improve the innovation ability; The coordination of relationship among government, school , enterprise, to achieve the rational division of school body, to create a good innovational environment; The reasonable classification of school level can improve running schools effectiveness, to achieve regional scientific and technology innovation. Only this way, it is possible to realize the concordance between the regional creative system and the regional higher education, and achieve regional products, industries and institution innovation.