Accompanied by the continuous diversification and evolution of market entities, a series of fundamental and practical major questions—such as who represents the public will, how to effectively promote and fairly distribute social resources, organize public production, and provide public endowments—urgently require systematic and in-depth exploration by both academia and society at large. As the third generation of development economics thought following structuralism and neoliberalism, the extension and application of New Structural Economics to the traditional field of public economics will bring about a profound structural transformation. This paper, grounded in the core dual logic of the capable government and the effective market, and building upon the structural analytical paradigm of New Structural Public Economics and the laws of economic structural dynamics it reveals, attempts to systematically construct a preliminary theoretical framework for New Structural Public Economics. Furthermore, it delves into the analysis of economic development, economic transformation, and the synergistic role of the effective market and capable government in economic operations, examining these from the output end of the public economic system through industrial structural transformation and the input end through factor endowment structure and public endowment structure transformation.