The farmland system in the global terrestrial ecosystem has dual attributes as both a carbon source and a carbon sink, playing a crucial role in controlling carbon emissions and mitigating global warming. Using carbon source and sink accounting of farmland ecosystems, we applied methods such as standard deviation ellipse, Tapio decoupling theory, and Markov chain to analyze the spatiotemporal changes, response mechanisms, and evolutionary trends of regional carbon effects. The results indicated that from 2011 to 2021, the farmland ecosystem in the middle and lower reaches of the Yangtze River consistently acted as a carbon sink. However, the net carbon sink showed slight fluctuations and significant spatial differences. The migration range of the net carbon sink center in the farmland ecosystem of the middle and lower reaches of the Yangtze River was relatively small, ranging from 115.52 to 115.77° E and 30.14 to 30.27° N. The decomposition of the Tapio decoupling index between the net carbon sink of the farmland ecosystem and agricultural output value showed the order of effects on their coupling relationship as follows: agricultural mechanization level > agricultural mechanization efficiency > agricultural output value > planting scale. The probability of maintaining the original state of net carbon sink in various cities in the middle and lower reaches of the Yangtze River (over 77%) was much higher than the probability of transfer, making it difficult to achieve a leapfrog growth in net carbon sink. The net carbon sink at the city scale exhibits the Matthew effect and spatial spillover effect. The above research results clarify the spatiotemporal changes in carbon effects in agricultural production at multiple levels, including city, province, and region. They also provide a theoretical basis for formulating differentiated regional emission reduction and sink enhancement strategies in the middle and lower reaches of the Yangtze River, promoting the rapid development of low-carbon agriculture in China.