The coordination of agricultural water use efficiency (AWUE) and the level of agricultural economic development (AEDL) is crucial for promoting high-quality development in the Qilian Mountains region. This study was aimed at examining the synergistic development trends and spatial distribution characteristics of AWUE and AEDL. This study focused on 11 cities (autonomous prefectures) within and adjacent to the Qilian Mountains region, employing the Super-SBM model and a comprehensive evaluation model to measure AWUE and AEDL. The coupling coordination degree model and coefficient of variation method were used to analyze the level of development coordination as well as spatial differences. The findings indicate that (1) from 2010 to 2022, both AWUE and the AEDL in these areas showed a significant upward trend, with AWUE increasing from 0.379 to 0.924 and AEDL rising from 0.284 to 0.437. The spatial analysis reveals a pattern of high values in the northeast and low values in other regions; (2) the coupling degree (CD) between AWUE and AEDL is in the primary coupling stage (0.456-0.474), with the coupling coordination degree (CCD) transitioning from low (0.401) to high coordination (0.554) between 2010 and 2022. The spatial distribution characteristics of the CD and CCD are high in the middle section and low in the eastern and western sections. Furthermore, the high coordination area exhibits a spreading evolutionary trend, from Zhangye City to Hexi Corridor regions, from the middle to the east and west sections, and from the north to the south section. These findings suggest that the coupling and coordination between AWUE and AEDL in the Qilian Mountains region have been improved, reaching a higher level. Combined with targeted suggestions, the findings offer valuable insights for designing targeted policies and water-saving measures to advance sustainable agricultural development in arid areas.