In the context of global warming, the acceleration of the water cycle increases the risk of meteorological drought (MD) and hydrological drought (HD) in the arid region of Northwest China. The Manas River Basin is a typical agricultural oasis and the largest oasis farming area in Xinjiang, Northwest China. Droughts in this basin have significant implications for both agricultural production and the livelihoods of inhabitants. To evaluate the MD and HD and provide information for drought relief in the MRB, the standardized precipitation evapotranspiration index (SPEI) and standardized runoff index (SRI) were calculated using long-term rainfall and runoff data. Subsequently, combined with ArcGIS 10.3 software and the trend analysis method, the SPEI and SRI characteristics were evaluated at different time scales (1-, 3-, 6-, and 12-month). There were three main findings. First, both MD and HD were alleviated, with significantly more HD alleviation. MDs in spring and autumn exhibited a trend of aggravation. The SRIs in summer, autumn, and winter increased significantly at a confidence level of p < 0.01, with an insignificant decline in spring. In the 2010s, the frequency of light drought of MD was stable at 10% to 20%, while severe and extreme droughts increased. The frequency of HDs has decreased since the 1990s. Second, on annual and seasonal scales, MDs occurred mainly as light and moderate droughts. The highest frequency of MD was 24% of moderate droughts in winter. Spatially, the northern region of the MRB was characterized by more frequent light and extreme droughts. Third, runoff in the Manas River Basin increased significantly during the 1990s, which may have been related to the acceleration of glacial retreat in the Tianshan Mountains. This study can effectively reveal the changes in meteorological and hydrological drought in NWC and provide the basis for risk decision-making and management for watershed managers.