Abstract:From the perspective of innovation value chain, the paper analyzes the scientific and technological economic dilemma of "Valley of Death" and "Darwinian Sea" and its causes, and analyzes the governance mechanism of effectively solving the dilemma under the digital economy. There are problems of “value chain break” and “knowledge fragmentation” in the innovation value chain, which leads to the disconnection and dilemma between knowledge innovation and technological innovation to product innovation. The industry-university-research cooperation mode at the practical level cannot balance the resources needed for continuous innovation because of organizational boundary constraints. Conflicts in the distribution of interests and power control make cooperation difficult to sustain.Under the digital economy, the establishment of new R&D institutions with independent legal personality to use digital technology for digital organization management and knowledge management can effectively solve this problem.By using the digital technology such as the Internet, big data, and blockchain to organize and manage, the new R&D institutions can solve the contradiction between the dynamic mechanism of the industry-university-research cooperation and the operational mechanism, and connect the three links of “knowledge innovation, technology innovation and product innovation”. To prevent the break of the innovation value chain and ensure the smooth flow of knowledge; at the same time, according to the needs of the market, the new R&D institutions can do knowledge mining, technology identification, integrated innovation, and matching with market demand for knowledge services, effective knowledge management to solve the problem of knowledge fragmentation, and promote knowledge innovation results effective conversion ."New R&D institutions + digital governance" has become the way to solve the dilemma of "death valley" and "Darwinian sea" in the science and technology economy. Digital organization management and knowledge management have become the method of governance.