Drought monitoring is an important scientific basis for drought impact evaluation and the selection of mitigation strategies. Since the drivers of drought vary among regions, there is no universal drought index applicable to different regions. The Shiyang River Basin, an inland river basin, located in Gansu Province, China, has a closed water cycle system. Drought is a dominant nature disaster for the sustainable development of the region. Thus, this is an ideal area to explore the suitability of drought-monitoring indices. Here, we took the Shiyang River Basin as an example, in order to explore suitable indicators for agricultural drought monitoring in inland river basins. This study assessed the twelve different widely used drought indices used for monitoring the impact of drought on crop growth, represented by net primary production (NPP). The results showed that the vegetation status-based drought indices (VCI and NVSWI) had the highest significant correlation (0.6 ≤ |R| ≤ 1, p < 0.05) on NPP, and the integrated drought indices (DSI and ISDI) had the strong significant correlation (0.4 ≤ |R| < 0.6, p < 0.1). These four indices are good indicators for agricultural drought monitoring. Studies based on these four indices showed that agricultural drought has a tendency to slow down from 1982 to 2020. This is inconsistent with the monitoring of drought indices based on the meteorological variables that show a trend of increasing drought. This is mainly due to the increased efficiency of water management and its use in inland river basins. This indicates that other water resource information, such as runoff, should be included to construct an integrated agricultural drought-monitoring indices in management intensive regions, such as in an inland river basin.