Measuring regional differences in agricultural green total factor productivity (AGTFP) provides a basis for policy guidance on agricultural green development in the Yangtze River Delta (YRD) region. By constructing a two-period Malmquist–Luenberger index under the carbon emission constraint, we measure the AGTFP of cities in the YRD region from 2001 to 2019. Furthermore, adopting the Moran index method and the hot spot analysis method, this paper analyzes the global spatial correlation and local spatial correlation of AGTFP in this region. Moreover, we investigate its spatial convergence. The results show that the AGTFP of 41 cities in the YRD region is on an increasing trend; the growth of AGTFP in the eastern cities is mainly driven by green technical efficiency, while this growth in the southern cities is mainly stimulated by green technical efficiency and green technological progress. We also find a significant spatial correlation between cities’ AGTFP in the YRD region from 2001 to 2019, but with certain fluctuations, showing a U-shaped trend of "strong-weak-strong". In addition, absolute β convergence of the AGTFP exists in the YRD region, and this convergence speed is accelerated with the addition of spatial factors. This evidence provides support for implementing the regional integration development strategy and optimizing the regional agricultural spatial layout. Our findings offer implications for promoting the transfer of green agricultural technology to the southwest of the YRD region, strengthening the construction of agricultural economic belts and agricultural economic circles, and improving the efficiency of agricultural resource use.