Abstract: To study research institutions’ competitive advantage in the super-competitive environment, this paper structured analyzes it from knowledge discovery and application. We select 102 institutes of Chinese Academy of Sciences as empirical test samples and get the following conclusions. (1) Competitive advantage of research institutions is a combination of resources and capabilities, which is able to maximize its long-term value. (2) Based on knowledge discovery, we need systematic and sustained accumulation study samples and continue to cultivate large sample / big data analysis capability for discovering the rules of development continuously. Based on knowledge application, the keys are to cultivate the abilities to solve major national strategic issues and transfer technological achievements. (3) Compared to the research institutions do not have a competitive advantage above-mentioned, the ones with the competitive advantage is more prominent in terms of performance value. (4) Research institutions for competitive advantage deletion, weakened or wandering should take different counter measures.