Achieving innovation-driven and endogenous growth are critical to the development of China’s modern agriculture. Modern agricultural science and technology innovation system, with the characteristics of publicity, sociality, diversity, systematism, and openness, is a strategic support for agricultural modernization and sustainable growth. It is also the endogenous driving force for the eliminating of the urban-rural dual structure and the overcoming of the shortcomings of agricultural modernization. However, China’s current modern agricultural science and technology innovation system is facing a series of challenges and problems, including the management system obstacles, the separation of agricultural research and production, the unsoundness of agricultural technique extension service system, the deficiency of incentive mechanism, and the risk compensation mechanism. Therefore, to establish and improve China’s modern agricultural science and technology innovation system, the paper suggests to adopt some optimized measures, including 1) establishing the synergistic innovation mechanism, 2) enhancing the cooperation among industry and education and research institutions, 3) constructing the dynamic mechanism, 4) accelerating the transformation of agricultural science and technology achievements, 5) building the integrated agricultural technique extension service system, 6) encouraging the innovation of agricultural research funding system, and 7) reforming and perfecting the commercial breeding mechanism.