The new national system reflects the strategic understanding of the modernization of major projects, and is an important weapon for major scientific and technological innovation in engineering. Major projects are characterized by multiple participants, interdisciplinary integration, long industrial chain, long construction cycle, high technical complexity, strong knowledge relevance, and high safety and quality standards. They have the typical characteristics of an ecosystem, namely, complexity, blending, and dynamic evolution. Therefore, it is of considerable theoretical significance and practical value to study complex major project innovation from the perspective of innovation ecology theory. The implications and composition of the innovation ecosystem of complex major projects are analyzed, focusing on the dependence and evolution of the relationship between innovation subjects. The role of the core leader and platform builder of large-scale central enterprises is highlighted, with the "win-win" concept as the core. Development and innovation promotion strategies are formulated, and the resource integration capacity and collaborative promotion of large-scale central enterprises are improved. Under the new national system, large-scale central enterprises must adapt to the development direction of emerging technologies,support for subjects in the ecosystem must be collaborative to realize the overall transition of the ecosystem, major engineering innovation platforms should be optimized, and the high-quality development of complex major projects must be promoted.