As a typical inland river basin in China, the Shiyang River Basin is characterized by its special mountain-basin structure. The ecological health in the basin is related to the sustainable development of the economy and society. At present, there are few studies on net primary productivity ($NPP$) in the Shiyang River Basin, and the existing analysis of the relationship between $NPP$ and climatic factors is lacking. The upper mountainous area and the middle and lower oasis areas in the Shiyang River Basin were selected as the study area. The $NPP$ of the study area was estimated using the Thornthwaite Memorial Model. The spatial and temporal characteristics of $NPP$ were analyzed by Sen’s slope method. Based on the sensitivity analysis, the correlation of the main climate factors to $NPP$ was estimated. According to the aforementioned work, the variation trend of the future $NPP$ was predicted. The results showed that $NPP$ in the study area increased from 1981 to 2015 with the increase in temperature and precipitation. The spatial heterogeneity of the change trend of $NPP$ was not significant, but the spatial heterogeneity of the rangeability was strong. The $NPP$ was highly sensitive to precipitation, relative humidity and net solar radiation. By integrating the changes in climatic elements, the temperature, precipitation and relative humidity contributed the main parts of the change in $NPP$. The $NPP$ is predicted to increase by 4.9–8.1% by 2050 according to the amplitude of climate change over the past 35 yrs.