Frequency and severity of droughts were projected to increase in many regions. However, their effects of temporal dynamics on the terrestrial carbon cycle remain uncertain, and hence deserve further investigation. In this paper, the droughts that occurred in China during 2001–2010 were identified by using the standardized precipitation index (SPI). Standardized anomaly index (SAI), which has been widely employed in reflecting precipitation, was extended to evaluate the anomalies of net primary productivity (NPP). In addition, influences of the droughts on vegetation were explored by examining the temporal dynamics of SAI–NPP along with area-weighted drought intensity at different time scales (1, 3, 6, 9 and 12 months). Year-to-year variability of NPP with several factors, including droughts, NDVI, radiation and temperature, was analyzed as well.