As one of the largest agricultural countries in the world, China has always paid close attention to the sustainable development of agricultural production efficiency. However, with global climate change, extreme weather has become an exogenous factor that cannot be ignored, as it affects agricultural production. Most of the existing studies only consider the domestic natural resources and economic factors, without fully considering the external climate factors. This paper uses the super undesirable dynamic Slacks-Based Measures (SBM) under an exogenous variable model to simulate the external environmental factors by adding extreme weather days. The Dagum Gini coefficient and kernel density estimation are used to explore the regional differences in agricultural production in China. The results show that the agricultural production efficiency is higher in the eastern region, and the difference in agricultural production efficiency among the provinces in the middle and western regions is large, showing a trend of polarization. The difference in the Gini coefficient between the middle and western regions is more significant. The main contribution factor of the Dagum Gini coefficient is the inter-regional difference. The regional concentration degree of agriculture in China is decreasing, the regional distribution of agricultural water resources is more balanced, and the national regional difference gradually decreases. Finally, some suggestions are put forward, such as extreme weather control, agricultural water supply, and water-saving measures.
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