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• China's sustainable development relies on agricultural trade and carbon emissions. • Carbon emission transfer index in agricultural trade is measured. • Decoupling-recoupling model and integrated prediction model are constructed. • A unified framework for trade, environment and technology is established. Under the new development pattern of domestic and international "dual circulation" in China, studying the relationship among green technology innovation, agricultural trade deficit (ATD) and carbon emission transfer embodied in agricultural trade (ATCT) becomes crucial for achieving coordinated and unified high-quality economic development and efficient environmental protection. Based on this, the paper uses environmental input–output model, "two-stage" decoupling and recoupling model, panel vector auto-regressive model, spatial econometric model and "rolling" Grey-BP neural network prediction model to explore present status of ATD, ATCT and their relationship, driving role of green technology innovation, as well as whether that relationship will be improving in the future. The results reveal the following: (1) China's ATD and ATCT show an increasing trend year by year, and their inter-provincial differences are gradually significant over time. The overall relationship between ATD and ATCT does not display ideally, which makes it necessary to quickly transform that relationship into reasonable and ideal state. (2) Green technology innovation has significant positive "U-shaped" and inverted "U-shaped" local effects on ATD and ATCT respectively, with a reasonable range of ATD reduction while ATCT increase valuing from 0 to 0.290, and has significant positive "U-shaped" spatial spillover effect on both without any reasonable range. The short-term effect of green technology innovation on coordinated promotion between ATD and ATCT is superior to the long-term one. (3) Green technology innovation has a significant regional heterogeneity. Regional differences must be taken into consideration seriously, and the measures adapted to local conditions are crucial. The role of fundamental and progressive green technology innovation has heterogeneity, which means that targeted development and utilization of green technology products are important. (4) Regardless of the time horizon, the relationship between ATD and ATCT will improve, which can provide a key step for coordinated development of economy and environment in agricultural trade. Therefore, in order for China to implement and promote further opening-up, reduce agricultural trade dependence, ensure food security and important agricultural product supply, as well as achieve the unity of high-quality economic development and ecological efficient protection, it is necessary to reasonably reverse trade deficit and increase carbon emission transfer in agriculture. [ABSTRACT FROM AUTHOR]