Organizational performance improvement is the important direction of deepening current R&D institutions management. But different sources of funding and their proportion have different influence on organizational performance. The allocation method of financial fund's overall budget is a new attempt to improve performance under the background of structured fund management. By analyzing the inner relationship between R&D organization performance and funding structured governance, this paper takes some international well-known institutions for examples,such as Fraunhofer in Germany and Taiwan institute in funding structured management experience,through the allocation method of financial fund's overall budget to explore and achieve the whole R&D deepening budget decision mechanism,achieve the goal of improving the research organization performance.