The quest to eradicate poverty, central to the United Nations Sustainable Development Goals (SDGs), poses a significant global challenge. Advancement in sustainable rural development is critical to this effort, requiring the seamless integration of environmental, economic, and governmental elements. Previous research often omits the complex interactions among these factors. Addressing this gap, this study evaluates sustainable rural development in China by examining the interconnection between agricultural production and government-led poverty reduction, with annual rainfall considered an influential factor of climate change impacts on these sectors and overall sustainability. Utilizing a Meta-frontier entropy network dynamic Directional Distance Function (DDF) within an exogenous Data Envelopment Analysis (DEA) model, we categorize China’s 27 provinces into southern and northern regions according to the Qinling-Huaihe line for a comparative study of environmental, economic, and governmental efficiency. This innovative approach overcomes the limitations of previous static analyses. The findings reveal: (1) Rainfall, as an exogenous variable, significantly affects agricultural production efficiency. (2) The overall efficiency in both southern and northern regions increases when accounting for rainfall. (3) Government effectiveness in poverty reduction is comparatively lower in the northern region than in the southern region when rainfall is considered. These insights underscore the importance of including climatic variables in sustainable development policies and emphasize the need for region-specific strategies to bolster resilience against climatic challenges.