Hub economy is a kind of emerging economic form. Developing a hub economy is essential to strengthen domestic and foreign connectivity and build a powerful country in transportation. This paper designs a two-stage analysis framework for the evaluation and impact study of the input-output efficiency of the hub economy based on the super SBM model, Malmquist model, and Tobit model. In the first stage, the Super SBM and Malmquist models are used to measure the static and dynamic efficiency of the hub economy. In the second stage, the Tobit model is used to analyze the factors influencing the efficiency of the hub economy. Among them, the explained variable in the second stage is the measurement result of technical efficiency in the first stage. The empirical results of 30 provinces and cities in China from 2012 to 2021 show that (1) the technical efficiency (TE), pure technical efficiency (PTE), and scale efficiency (SE) of China’s hub economy are 0.585, 0.740, and 0.820, respectively, which do not reach the effective state; (2) the technical efficiency change index (Effch), technical progress change index (Techch), and total factor productivity change index (Tfpch) of China’s hub economy are 0.994, 0.945, and 0.939, respectively, indicating that the corresponding efficiencies show a downward trend; and (3) industrial structure, innovation, and technology are significantly and positively correlated with the efficiency of the hub economy; policy and enterprises are significantly negatively correlated with the efficiency of the hub economy; and education does not correlate with the efficiency of the hub economy.