Abstract: Black soil serves as the core foundation of China’s primary grain-producing regions and the strategic cornerstone of grain security. As a scarce arable resource essential for ensuring high and stable grain yields, its scarcity and non-renewable nature dictate the urgency of conservation efforts. A scientifically sound and comprehensive institutional system is the core support for achieving long-term protection. This study systematically analyzes the unique attributes of the black soil protection institutional system distinct from the cultivated land protection, guided by core theories including the genetic pedology of black soils, the valuation theory of black soil land and the theory of ecological balance. Drawing on the collaborative protection experience of the “government, market, society” model in the United States, it examines the legal foundations and practical challenges of black soil protection in China. Ultimately, it constructs a trinity institutional system comprising “responsibility protection, resource management and conservation, and support and safeguards.” Research indicates that black soil currently faces challenges of quantitative, qualitative, and systemic ecological degradation. Existing protection systems suffer from fragmentation and insufficient specialization, limiting their effectiveness. In addition, this study systematically reviews the existing black soil protection mechanisms to establish a comprehensive institutional system for China. Based on the above analysis, this paper suggests that the responsibility protection system must delineate the rights and responsibilities of multiple stakeholders, the resource management and conservation system must focus on coordinated management of quantity, quality, and ecological integrity, and the support and safeguard system must strengthen synergistic technical and financial backing. This framework also provides a reference for refining and optimizing China’s black soil protection system.