Abstract: In the context of building a strong agricultural nation, the seed industry, which serves as the cornerstone of agriculture, plays a vital role in promoting high-quality agricultural development. Although China’s seed market is gradually shifting toward mergers between seed and agrochemical enterprises, it is still mainly characterized by internal horizontal consolidations. Despite continued integration efforts, market concentration remains low, and the industrial chain exhibits weak connectivity, particularly between research and development and production. Inadequate intellectual property protection further restricts coordinated development across the industry. To address these challenges, this study proposes a modern seed industry innovation framework that focuses on strengthening leading enterprises, integrating breeding, propagation, and promotion, enhancing intellectual property protection, and promoting collaborative innovation among multiple stakeholders. By advancing resource integration, accelerating key technological breakthroughs, and optimizing the financing environment, the proposed framework aims to enhance the market competitiveness and innovation capacity of the seed industry. This will help achieve efficient coordination across the entire industrial chain and promote the sustainable and healthy development of a modern seed industry.