Abstract: According to the research from three state-owned diversified group companies in Shaanxi Province, it can be found that in the traditional R & D funds management mode, due to the constraints of the system itself, there has been insufficient corporation R & D strength, inefficient use of R & D funds, various group companies for R & D input power shortage and other issues, which affect the company and the country's technological breakthroughs and technological development. This article, from the perspective of the new institutional economics, analyzes the traditional R & D funds management problems, finds ways to change the problem to establish a market-oriented R & D funds management system, puts forward the path selection of the new system, and analyzes possibilities of institutional innovation.