Abstract: To facilitate agricultural green transformation and support the “Dual Carbon” goals, it is crucial to understand how farmland transfer affects agricultural green total factor productivity (AGTFP). Using panel data from 30 Chinese provinces (excluding Xizang, Hong Kong, Macao, and Taiwan) from 2005 to 2023, this study measures AGTFP by applying the SBM-GML super-efficiency model that incorporates agricultural non-point source pollution. It then employs a two-way fixed effects model, alongside with moderating and threshold effect models, to empirically analyze the impact of farmland transfer on AGTFP and its underlying mechanisms. The findings are as follows: 1) farmland transfer enhances AGTFP primarily through technological progress; 2) this positive effect is more pronounced in eastern regions, major grain-selling areas, and under small-scale farming conditions; 3) the agricultural cropping structure negatively moderates this relationship, mainly by inhibiting technological progress; and 4) the promoting effect of farmland transfer diminishes once its scale exceeds a certain threshold. These findings suggest that accelerating the marketization of farmland transfer, promoting institutional innovation for moderate-scale operations, strengthening the diffusion of modern agricultural technologies, and optimizing cropping layouts are key to fostering green transformation and high-quality agricultural development.