[Objective] The trade-off and coordination between agricultural ecological efficiency and economic resilience in arid regions and their driving factors were identified, in order to provide a scientific basis for achieving regional sustainable development and win-win management decisions for agricultural development and ecological protection in Xinjiang. [Methods] Agricultural ecological efficiency levels and agricultural economic resilience in 14 prefectures of Xinjiang Uygur Autonomous Region from 2010 to 2022 were measured. Spearman’s rank correlation analysis, production possibility frontier (PPF), and trade-off intensity index were employed to quantitatively analyze the trade-off and coordination relationships between efficiency and resilience. Geographically weighted regression (GWR) was applied to analyze the influencing factors of the efficiency-resilience trade-off and coordination relationships in different regions. [Results] ① The agricultural economic resilience in Xinjiang demonstrated a rapid growth trend over time and a spatial distribution pattern of “south > north”. Agricultural ecological efficiency showed an increasing trend, with a spatial pattern of “south > north”. ② Output and resistance demonstrated significant coordination, while output and recovery exhibited significant trade-off. The PPF curves of input—resistance and output—recovery were “concave-down—convex-up” in shape, with most of the corresponding combinations in their optimal configurations. ③ The trade-off relationship between efficiency and resilience was strengthened by all influencing factors, with the overall order being: fiscal expenditure on agriculture, forestry, and water resources > fiscal expenditure on science and technology > total output value of agriculture, forestry, animal husbandry, and fishery> total investment in environmental pollution control. Additionally, the influencing factors enhanced the coordination relationship between efficiency and resilience in the following descending order: total investment in environmental pollution control> fiscal expenditure on science and technology > total output value of agriculture, forestry, animal husbandry, and fishery> fiscal expenditure on agriculture, forestry, and water resources. [Conclusion] All prefectures in Xinjiang should formulate region-specific policies for the trade-off and coordination between agricultural ecological efficiency and agricultural economic resilience, thereby achieving sustainable development in arid regions.