Science and technology innovation is the key to develop seed industry. Beijing is one of the regions with science and technology foundation, concentrated innovation resources and active innovation subjects in China’s seed industry. This paper compared scientific and technological innovation of Beijing with developed countries from 4 aspects including germplasm resources, breeding technology, R&D mode and competitiveness of seed enterprises, and systematically analyzed the key problems that restricted the scientific and technological innovation of Beijing seed industry. This paper focused on scientific and technological innovation, and put forward some suggestions to promote the scientific and technological innovation of Beijing’s seed industry from the aspects of strengthening the protection and utilization of germplasm resources, taking joint research on key breeding technologies, deepening the reform of seed industry system, improving the policy support system for breeding innovation, and promoting the joint forces between ministries and municipalities. It was expected to provide reference for technological innovation of the national seed industry.