With the rapid development of China’s economy, China’s technological strength has also made significant improvements. As the main engine for the innovation and development of national defense technology, military research institutes have made tremendous contributions to improving equipment performance and technological innovation in China, and playing a vital role. However, under the overall guidance of the strategy of building a strong country through science and technology, there are certain deficiencies in the technological innovation capabilities of China’s military research institutes compared to relevant organizations in the United States, such as collaborative innovation, generation and management of cutting-edge technology projects, and transformation of achievements. Therefore, this paper takes DARPA and DIU, the pioneers of defense technology innovation in the United States, as the research objects. The unique features and success oaths of DARPA and DIU are identified through analysis through comparative analysis of their organizational structures, operational mode, prominent advantages, and related measures. Based on the current development status of military research institutes, relevant suggestions for scientific and technological innovation in military research institutes are proposed from a macro level. Specific recommendations and measures are proposed from the perspectives of improving the scientific and technological collaborative innovation system, constructing the generation and management mechanism of innovative cutting-edge scientific and technological projects, enriching the strategic research expert committee and improving relevant mechanisms, and playing the role of the expert committee, providing a reference for the development of scientific and technological innovation in military research institutes.