Abstract By constructing a twotier heterogeneity stochastic frontier model and taking listed companies in Hubei province as samples, this paper quantitatively investigates the direction and extent of financing constraints and agency costs on the inefficient R&D investment of enterprises. The results show that: first, financing constraints and agency costs have an important impact on R&D investment of enterprises, among which, financing constraints have more influence on R&D investment of enterprises than agency costs. Second, on the whole, investment in R&D of Hubei enterprises is 18.05% lower than the optimal level, but about 32.84% of companies invest more than the optimal R&D investment, and about 59% of companies invest less than 10% in R&D investment. Third, the heterogeneity of inefficient R&D investment is strong, and the local stateowned enterprises and nonpublic enterprises is generally underR&D Investment, however, the R&D investment of central stateowned enterprises is more efficient. The effective play of the role of "hand of government" in innovation leading should consider the categorization and decisionmaking to different enterprises and precise guidance.