Abstract: The current scientific and technological innovation is showing a new trend of dual integration, accelerating its integration with economic and social development, and interdisciplinary integration. Therefore, innovation in the organizational model of scientific and technological research activities has become a key link in promoting research paradigm transformation and solving systemic and complex problems, which has become increasingly prominent in the high-quality development of major national strategic regions. Focusing on the needs of building a beautiful China in the new era and achieving self-reliance in green and low-carbon technology development, this study analyzed the concept and contemporary connotation of the New National Mechanism for Scientific and Technological Research on Eco-Environment (NNM-STREE). In view of the characteristics of social-economic-environmental complex system, five kinds of basic characteristics of major sci-tech project management as well as five major barriers of major scientific research activity management in the field of eco-environment were first analyzed. Based on traditional engineering management theory and combined with the advantages of national institutions, the NNM-STREE framework was then constructed, forming the theoretical thinking on the "1+X" DSE (decision-support-execution) system architecture and organization methods. Case studies in the Beijing-Tianjin-Hebei region, the Yangtze River basin, and the Yellow River basin have shown that by constructing a multi-level and three-dimensional "1+X" organizational model, a "collaborative combat style" scientific and technological breakthrough has been achieved. The organizational, regional, information, technological, and disciplinary barriers that previously existed in major scientific research activities have been broken down, and sci-tech collaborative innovation has been achieved. Meanwhile, these also promoted a collaborative regional eco-environment governance system with scientific research closely incorporated, achieving significant results.