Building an agricultural powerhouse hinges on technological advancement and institutional reform. Against the backdrop of the ongoing seed industry revitalization initiative, constructing a comprehensive biological breeding innovation system from a systemic perspective and enhancing overall innovation efficiency have become key pathways to ensuring national food security. Grounded in the current state of China’s biological breeding technologies and industrial development, this study adopts theoretical deduction and comparative analysis methods, incorporating insights from existing research on national innovation systems, regional innovation systems, and agricultural science and technology innovation systems. Focusing on the technological evolution toward the Intelligent Breeding 5.0 era in the modern seed industry and drawing on international experiences from leading seed powerhouses, the study innovatively defines the concept of the “biological breeding innovation system”. It further analyzes the roles and interactions of five key innovation actors (government, industry, academia, research institutes, and intermediaries), revealing how a spiral mechanism driven by multi-agent collaboration enhances innovation efficiency. By applying the theoretical framework of “Four-Chain Integration” (innovation chain, industrial chain, capital chain, and talent chain), this study systematically elaborates on how the optimized allocation and coordinated evolution of these four chains jointly drive improvements in biological breeding innovation efficiency. The “Nanfan Silicon Valley” is presented as a representative case, vividly illustrating the practical path and effectiveness of the “Four-Chain Integration” model. Finally, the study outlines future research directions aimed at building an institutionalized, standardized, systematic, and sustainable biological breeding innovation system, with the goal of providing theoretical support and practical reference for breakthroughs in biological breeding technologies and the high-quality development of China’s seed industry.