Background: The Yangtze River Economic Belt (YREB) occupies an important economic position in China and has great research value. Methods: Based on the panel data of 142 GEM-listed companies in the YREB from 2015 to 2019, using the DEA Malmquist index, σ-convergence and β-convergence models, this study empirically analyzes the dynamic change and convergence trend of the innovation efficiency of these companies. Results: The number of these companies increased significantly but the innovation efficiency of them has not reached the optimal level. From a static point of view, companies in the middle reaches of the Yangtze River have the highest innovation efficiency, while from the dynamic point of view, the Yangtze River Delta region has the highest innovation efficiency. Moreover, most companies have an agglomeration effect, and there is a big gap in innovation efficiency. There is no σ-convergence trend in the YREB and its sub-regions, but there is an obvious β-convergence trend. Conclusions: The innovation efficiency of these companies has a lot of room for improvement. There is industry heterogeneity, and exogenous factors have different effects on the improvement of innovation efficiency in different regions owing to the differences in geographical location, economic development level, and other factors.