Accurate assessment of green productivity is essential for advancing sustainable agriculture in ecologically fragile regions. This study examined the evolution of agricultural green total factor productivity (AGTFP) in Tibet over the period 2002–2021 by applying a super-efficiency SBM-GML model that accounts for undesirable outputs. We decompose AGTFP into technical change and efficiency change, conduct redundancy analysis to identify sources of inefficiency and explore its spatiotemporal dynamics through kernel density estimation and convergence analysis. Results show that (1) AGTFP in Tibet grew at an average annual rate of 0.78%, slower than the national average of 1.6%; (2) labor input, livestock scale, and agricultural carbon emissions are major sources of redundancy, especially in pastoral regions; (3) technological progress is the main driver of AGTFP growth, while efficiency gains have a limited impact, reflecting a technology-led growth pattern; (4) AGTFP follows a “convergence-divergence-reconvergence” trend, with signs of conditional β convergence after controlling for regional heterogeneity. These findings highlight the need for region-specific green agricultural policies. Priority should be given to improving green technology diffusion and input allocation in high-altitude pastoral areas, alongside strengthening ecological compensation and interregional coordination to enhance green efficiency and promote high-quality development across Tibet.

This study employs a Super-SBM model to construct a comprehensive evaluation framework—encompassing input factors, desirable outputs, and undesirable outputs—to measure agricultural green total factor productivity (AGTFP) in the Tibet Autonomous Region in the period 2002–2021. We then apply kernel density estimation and Dagum Gini coefficient decomposition to examine its spatiotemporal evolution. The main findings are as follows: (1) AGTFP in Tibet rose overall from 0.949 in 2002 to 1.068 in 2021, with a compound annual growth rate of 0.78%, yet remained below the national average; (2) significant regional heterogeneity emerged, with three typical evolution patterns identified: continual improvement (Nagqu, Qamdo), stable fluctuation (Lhasa, Xigazê), and risk of decline (Lhoka, Nyingchi, Ngari); (3) gains in pure technical efficiency were the primary driver of AGTFP growth, while insufficient scale efficiency was a key constraint; (4) AGTFP exhibited a “convergence–divergence–reconvergence” dynamic, with interregional disparities widening but structural patterns stabilizing; and (5) interregional inequality was the main source of overall disparity—its importance grew over the study period, with the largest gap observed between agrarian and pastoral zones. On this basis, we recommend a “gradient advancement” strategy that prioritizes pure technical efficiency and regional coordination, while promoting zone-specific support tools tailored to local ecological conditions and institutional capacities to ensure inclusive green productivity growth.