Based on the perspective of the value chain of agricultural science and technology innovation, in this paper, we divided the process of agricultural science and technology innovation into two stages: the Research and Development (R&D) of agricultural technology and the application of agricultural technology. We took the efficiency of agricultural science and technology innovation of the two stages as a comprehensive index measure for the development of agricultural science and technology innovation in China. On this basis, we used social network analysis to establish a two-stage spatial correlation network for the innovation development of agricultural science and technology in China. The spatial-temporal evolution trends, structural characteristics, and influencing factors of the network were analyzed from the three aspects of the overall, local, and individual network structure. The results show that: a. The development of agricultural science and technology innovation in China demonstrated a clear spatial correlation and spillover effect, and the spatial correlation network was in a connected state. b. The network had the distribution characteristics of ‘core-edge’ and strong stability, and the hierarchical structure of the members of each province in the network was gradually broken. c. The differences at the market level in agricultural science and technology, the differences in government support for agriculture, the geographically adjacent relationships, and the level of agricultural economic development were important factors affecting the spatial correlation of agricultural science and technology innovation. This study provides a policy reference to use a cross-regional coordinated development mechanism to solve the uneven and asymmetry problem of the distribution of elements in various regions in China.