Seed industry is a strategic and basic industry, and clarifying the development path of China’s crop seed industry is very important to enhance the competitiveness of national agriculture. This paper analyzed the development trend of the international crop seed industry, assessed the opportunities and challenges faced by the development of China’s crop seed industry, and proposed the innovative development strategies of China’s crop seed industry in the new era. Our study reckoned that the new round of scientific and technological revolution characterized by “biotechnology and informatization” had promoted the comprehensive upgrading of the crop seed industry, biotechnology productions had become an important growth point for the development of the seed industry, and multinational seed enterprises had accelerated their occupation of the global seed market. Global scientific and technological innovation and China’s economic transformation and development have brought new opportunities for the development of China’s crop seed industry. Currently,China has basically established a scientific and technological innovation system for crop seed, and seed enterprises have continued to grow, but still facing some challenges such as insufficient original innovation in key science and technology, imperfect seed industry innovation system. Our study suggested that China’s crop seed industry should further strengthen the effective cohesion in the innovation chain and build a deep integration system of production, education and research in the new era, and consolidate the original foundation of seed science and technology, produce high-value intellectual property rights such as key technologies and elite new varieties, as well as cultivate innovative enterprises, improve policy mechanisms and business environment, and promote the high-quality development of the crop seed industry.