This paper investigates the temporal trend and regional disparity of China’s agricultural green total factor productivity (AGTFP) during 1997-2016. Combined with the green Luenberger productivity indicator, two different data envelopment analysis models with the biennial environmental technology are constructed for robust checks. Compared with the existing literature, more agricultural carbon emissions are used as the undesirable outputs in the models. It is found that AGTFP in the whole of China and all of its sub-regions (the east, the middle, and the west) showed an overall increase, with the drive of high technical progress. The east had the largest AGTFP, and the middle experienced the largest AGTFP growth. More specifically, with respect to AGTFP, the total difference and the gross difference among the three regions as well as the specific difference within regions widened during these periods. There was an absolute convergence trend of AGTFP in the whole of China as well as the middle and the west. The speed of convergence was highest in the west.