Abstract: In order to achieve efficient water use and promote green agricultural development. This study utilizes a dynamic SBM-DEA model, which accounts for undesirable outputs, to measure the agricultural ecological efficiency of 30 provinces (autonomous regions and municipalities) and eastern, central and western regions in China during 2011~2022, and employs fixed-effect and moderating effect models to explore the impact of water resource reallocation from agriculture to non-agriculture on agricultural ecological efficiency, as well as the moderating roles of agricultural water use efficiency and the trend of grainoriented crop planting. The results show that: (1) From 2011 to 2022, China’s agricultural ecological efficiency exhibited a fluctuating upward trend, with significant regional disparities, and eastern regions demonstrated higher efficiency compared to central and western areas. (2) Water resource reallocation from agriculture to non-agriculture has a significant negative impact on agricultural ecological efficiency. The improvements in agricultural water use efficiency mitigate this adverse effect, and the trend toward grain-oriented planting intensifies the negative impact of water resource reallocation on ecological efficiency. Based on this, it is proposed to control the scale of resource reallocation, enhance the regulation of water reallocation, optimize water resource utilization efficiency, promote water-saving technology, optimize the planting structure on the basis of ensuring food security, and strengthen agricultural ecological protection and development in the western region, in order to improve the overall agricultural ecological efficiency.