The leadership of Party building in guiding the “Three New” organizations to participate in efficient grassroots governance is the essential path for upholding the Party’s overall leadership to achieve modernization of grassroots governance in the new era. It is also a strategic measure to consolidate the Party’s ruling foundation and enhance effective governance in emerging fields. By constructing a systematic theoretical analysis framework of “element-structure-function-evolution”, this paper clarifies the intrinsic logic of Party building in leading the “Three New” organizations to participate in grassroots governance. The framework considers Party organizations, “Three New” organizations, grassroots governments, communities, and residents as the core elements; policies, funds, information, and talents as key resource elements; and social, economic, and cultural environment as important external elements. Through the synergistic coupling of organizational, institutional, and network structures, it achieves core functions of integrating resources, serving the public, and optimizing governance, and reveals a dynamic evolution process from “tangible coverage” to “effective coverage”, from scattered participation to collaborative governance, and from management-oriented to service-oriented approaches. Currently, the process of Party building leading the “Three New” organizations to participate in grassroots governance faces the following problems, such as fragmented resources, low operational efficiency, passive participation, and outdated models. Therefore, it is necessary to adhere to a systems-thinking approach, focusing on step-by-step optimization in terms of comprehensiveness, structural design, openness, and dynamism, thereby constructing an organic entity for collaborative governance, establishing a hierarchically clear governance system, promoting the effective integration of multiple stakeholders, and adapting to environmental changes for continuous optimization. The goal is to achieve deep integration of Party leadership with the development of “Three New” organizations and to improve an efficient grassroots governance model characterized by co-construction, co-governance, and sharing, providing practical references and theoretical support for the high-quality development of Party building in emerging fields in the new era.