Abstract: Activating the positive traction of green technological innovation to promote the improvement of the green total factor productivity in agriculture has become a major practical issue of widespread concern among both the government and the academic community. Based on panel data of 258 prefecture-level cities across the country from 2004 to 2023 and applying the super-efficiency SBM-GML model, this paper calculates and analyzes the agricultural green total factor productivity. Furthermore, this paper also empirically examines the impacts, heterogeneity and internal mechanism of green technological innovation on agricultural green total factor productivity. The research findings indicates: 1) From 2004 to 2023, China’s agricultural green total factor productivity increased from 0.946 to 1.030, showing an overall upward trend; the high-value areas of agricultural green total factor productivity show scattered local agglomeration in Northeast China, North China, East China, Central China, Southwest China and Northwest China, and gradually expand to the southeast coastal areas as well as northern and southwestern peripheral regions, forming a spatial pattern of nationwide extensive distribution; 2) Green technological innovation can significantly promote the growth of agricultural green total factor productivity. After endogeneity correction and multi-dimensional robustness tests, this core conclusion remains reliable; 3) Green technological innovation has a significant promoting effect on the agricultural green total factor productivity in the eastern region, major grain-consuming areas, and regions with a focus on crop cultivation; And 4) green technological innovation boosts the green total factor productivity of agriculture by promoting agricultural industrial agglomeration and advancing the high-endization of the agricultural industrial structure. Subsequently, to continuously release the long-term empowering effect of green technological innovation on the green total factor productivity of agriculture, this paper suggests that efforts should be focused on multiple aspects such as benchmark demonstration leadership, core technology breakthroughs, regional differentiated adaptation, construction of innovation carrier platforms, and cultivation of new green agricultural business forms.