To clearly describe the structural characteristics of China’s rare earth innovation network (REIN), this study used data on China’s rare earth patents since 2001 in the Incopat global patent database to analyze the structural characteristics of China’s REIN from 2001 to 2020 at the provincial and municipal levels using social network analysis. The study finds the following: (1) The overall characteristics of the network show that the connectivity and diversification of China’s REIN is increasing. (2) The network spatial pattern analysis shows that the REIN exhibits a radial spatial pattern centered on Beijing at both the provincial and municipal levels. (3) Research on network nodes shows that the network is dense in eastern regions and sparse in western regions, showing distinct characteristics of coastal and resource agglomeration. Not all regions with high levels of economic development play leading roles in the REIN. Small and medium-sized cities with abundant rare earth resources also play important leading roles due to their high levels of rare earth innovation. At the provincial and municipal levels, the REIN consists of four subgroups, among which there is not significant factional diversity. (4) In terms of influencing factors, economic development level, technology absorptive capacity, innovation output level, infrastructure, and market leadership have significant impacts at the provincial and municipal levels. In addition, government leadership, industrial structure, and education level have significant impacts at the municipal level. The study clarified China’s technological accumulation in the field of rare earths and provided practical guidance for the innovative development of China’s rare earth industry.