Abstract: Technology is the driving force behind agricultural modernization. And the effectiveness of innovation and its optimal path are crucial topics for building an agricultural powerhouse. This study focused on publicly listed companies involved in agriculture in the Yangtze River Basin from 2017 to 2022. Data Envelopment Analysis (DEA) was employed to evaluate the innovation efficiency of each company. The Malmquist index model was then used to investigate the changing trends of technological innovation efficiency in terms of both time and space over the six-year period. Furthermore, a Tobit model was applied to analyze the factors affecting technological innovation efficiency. Studies had found that, agricultural firms listed on the Yangtze River Basin were characterized by low rates of progress, an increase in the number of individuals with master’ s degree or higher, and an insufficient positive impact of government subsidies on technological innovation efficiency. Policy recommendations included increasing R&D investment, rationally optimizing the scale structure, intensifying talent acquisition and cultivation, and improving the structure of government subsidies.