Understanding how industrial agglomeration affects agricultural green production efficiency is essential for green agricultural development. This study uses the super-efficient Epsilon-Based Measure (EBM) model and Global Malmquist–Luenberger (GML) index to measure and analyze the spatial and temporal evolution characteristics and core sources of dynamics of agricultural green production efficiency in China by using panel data from 30 Chinese provinces from 2006 to 2020. It also empirically investigates the relationships between industrial agglomeration, land transfer, and agricultural production efficiency. By using fixed, intermediary, and threshold effect models, the internal links between industrial agglomeration, land transfer, and agricultural green production efficiency are examined. The findings indicate the following. (1) The green production efficiency of Chinese agriculture exhibits the regional characteristics of being “high in the west and low in the east, high in the south and low in the north” in terms of space; in terms of time, the overall trend is that green production technology efficiency is growing, with an average annual growth rate of 11.45%, and the growth primarily depends on the “single-track drive” of green technological progress. (2) Industrial agglomeration significantly affects agricultural green production efficiency, green technology efficiency, and green technology change; the corresponding coefficient values are 0.115, 0.093, and 0.022. (3) According to the mechanism-of-action results, land transfer mediates the effects of industrial agglomeration on agricultural green production efficiency, green technology efficiency, and green technology change. These effects have effect values of 28.48%, 27.91%, and 47.75%, respectively. (4) The threshold effect’s findings demonstrate a double threshold effect of industrial agglomeration on the green production efficiency of agriculture in terms of land transfer, with threshold values of 1.468 and 3.891, respectively. As a result, this study suggests adhering to the idea of synergistic development, promoting agricultural green development, strengthening the development of industrial agglomerations, promoting the quality and efficiency of industry, improving land-transfer mechanisms, and placing a focus on resource efficiency improvements, as well as other policy recommendations.