The level of development of the innovation factor plays a crucial role in supporting the high-quality development of China's economy. To advance the development of regional innovation factor allocation efficiency along the Belt and Road. This article introduces the super-efficiency SBM-DEA-Malmquist model for the static and dynamic analysis of innovation factor allocation efficiency in 17 provinces along the Belt and Road from 2012 to 2021. The Moran index model analyzes the spatial correlation. The results show that: (1) The overall innovation factor allocation efficiency along the Belt and Road is not high, and there are obvious differences among different regions. The eastern region is the highest compared to other regions. (2) According to the efficiency decomposition results, pure technical efficiency is the main reason for the low innovation factor allocation efficiency. (3) Through the Malmquist index and decomposition index, it is found that pure technical efficiency and scale efficiency are key factors in improving technical efficiency. (4) The analysis of spatial correlation reveals a strong spatial agglomeration feature among the provinces along the Belt and Road. The innovation factor allocation efficiency is mainly manifested in the L-L type. Finally, according to the analysis results, suggestions and policies are put forward to improve the innovation factor allocation efficiency in the regions along the Belt and Road.