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<div><p>As China’s second-largest source of greenhouse gas emissions, agriculture is essential to achieving the goal of "carbon peak" and "carbon neutrality." Based on the measurement of agricultural carbon emissions (ACE) and agricultural carbon intensity (ACI) in 19 regions along the Yangtze River Economic Belt (YEB) and Yellow River Basin (YRB) in China from 2001 to 2020, this paper first uses the super-efficiency SBM model to measure ACE efficiency from static and dynamic perspectives. Then, the coupling coordination degree (CCD) between ACE efficiency and green finance in each region of the two basins is explored. Finally, Grey Relation Analysis (GRA) is used to obtain the influencing factors of CCD. The following conclusions are drawn: (1) The ACE in the YEB is almost twice that of the YRB. The ACE of the two basins generally experienced a trend of first growth and then declined, but the peak time was different. The ACI of the two basins showed a trend of continuous decline, and the decline rate of the YRB was faster. (2) The ACE efficiency of the two basins showed an overall upward trend, and the growth degree of different regions was vastly different. From the factor decomposition, the technological progress (TP) of the two basins significantly impacts the total factor productivity (TFP). (3) The CCD of ACE efficiency and green finance in the two basins increased from near imbalance to barely coordination level, and the CCD of the YEB increased slightly faster. The CCD of the two basins has a spatial difference of "downstream > midstream > upstream." (4) Among the influencing factors of the CCD of the two systems, the influencing degree of the factors is as follows from large to small: quality of human capital, level of economic development, government regulation, scientific and technological innovation ability.</p></div>