Economic agglomeration plays an important role in China's social transformation process of industry feeding agriculture and urban supporting rural areas, and is one of the core weapons to promote agricultural economic growth and green and efficient development. Based on panel data of 41 cities in the Yangtze River Delta (YRD) from 2010 to 2020, this paper constructs an “environment-resource-energy-economy” agricultural input-output system, taking into account carbon emissions and surface pollution, and provides a more comprehensive accounting of agricultural green total factor productivity (AGTFP), the non-linear effects of economic agglomeration on AGTFP and shock responses were empirically analyzed using a panel threshold model and a panel vector autoregression (VAR), respectively. The findings show that: (1) during the period 2010–2020, the AGTFP in the YRD showed an overall rising trend with regional spatial agglomeration characteristics. (2) Economic agglomeration has a triple threshold effect on AGTFP, which was a weak facilitative effect in the early stage, inhibited by the siphoning effect of resource loss and arable land fragmentation in the growth stage, promoted by the radiation effect of external increasing return to scale in the form of sharing, matching and learning in the maturity stage, and finally tends to decline. (3) The shock response of economic agglomeration to AGTFP showed a continuous positive shock, peaking in the first period and then gradually converging to zero. (4) The heterogeneity analysis demonstrated that economic agglomeration has a considerable impact on boosting AGTFP in non-metropolitan areas and cities on the outskirts of YRD. In the future, China should effectively play a positive role in economic agglomeration on AGTFP and enhance the mutual coordination of economic agglomeration and agricultural green development in the process of urban cluster economic growth.