The Shiyang River Basin is one of three large continental river basins in Hexi Corridor and is the region facing the greatest pressure on water resources. The utilization efficiency of water resources not only affects sustainable socioeconomic development but also affects the ecological security of the country. The irrigated area is the largest water consumption area in an arid inland river basin and is also a highly controversial multiuse area; therefore, comprehensive watershed management is fundamental in this area. Water-use efficiency has a profound effect on oasis stability and harmonious socioecological and productive developments in such areas. The present study used the DEA model, and we measured the agricultural water efficiency and its influencing factors in 13 irrigated areas of the Shiyang River Basin during 2000-2010. The results showed obvious temporal and spatial differences in water-use efficiency in irrigated areas before and after integrated measures. The water-use efficiency fluctuation noted during the early stages of management became more stable by 2007. The water-use efficiency of the irrigated areas were as follows:W-S irrigated areas in the middle reaches (taking wells and springs as irrigated water sources) > R irrigated areas in the middle reaches (taking rivers as irrigated water sources) > R-W-S irrigated areas in downstream(taking rivers、wells and springs as irrigated water sources), reflecting the strong influence of the watershe comprehensive measures. The key control region showed higher water-use efficiency than the non-key areas, but that of the downstream Hongyashan Reservoir Irrigated Area was still very low. The irrigated areas had different degrees of water and land redundancies;The redundancy of water-use in the W-S irrigated areas are more than the R irrigated areas, however, its redundancy and slack variables are decreasing, which indicates that the water resources conservation degree are strengthened after the integrated management. Before integrated management, the redundancy of irrigated land in the W-S irrigated areas and R-W-S irrigated areas were most; after, the redundancy were reduced, reflecting that "closing wells" and "compressing farmland" plays an obvious role.