Recently, drought events have occurred frequently and have profoundly altered the carbon sequestration in terrestrial ecosystems. How drought affects carbon sequestration is an important issue which may assist in understanding and confronting the challenges of extreme climate change. Nevertheless, drought-induced carbon-cycle effects remain scarce from the perspective of drought indices. In this study, we quantified the impacts of potential evapotranspiration (PET), standardized precipitation evapotranspiration index (SPEI), downward short-wave radiation flux (SWDown), and soil water (Soil_w) on net ecosystem productivity (NEP). We showed that the spatiotemporal heterogeneity of drought was extremely significant, and the hot spots of aridification were mainly distributed in the southwestern Yungui Plateau (YG) and Northwest China (NW). Moreover, the “pan evaporation paradox” appeared across the Chinese mainland before the 1990s and subsequently disappeared. Similarly, in contrast to the moderate NEP fluctuation between 1981 and 1999, since the beginning of the 21st century, NEP has increased significantly across Chinese mainland, YG, the plains region of Changjiang (CJ), and Southeast China (SE). Meanwhile, there are obvious directional, temporal, and spatial differences in the effects of the drought indices on NEP. Specifically, a higher SPEI value results in a more obvious promoting effect on NEP in SE, North China (NN), and northeastern YG. An increase in SWDown can promote an increase in NEP, especially in the northeastern YG and central SE. The increase in Soil_w in parts of the Qinghai-Tibetan Plateau, Xinjiang Region (XJ), southeastern NW, NN, and Northeast China with poor water conditions can promote carbon sinks. The inhibition effect is particularly obvious in some areas of CJ, where water resources are abundant. The fluctuation in PET has a relatively low influence on NEP. This study provides a comprehensive assessment of drought change and its impact on carbon sequestration and may help in formulating appropriate policies for carbon management and ecological security.