The potential impact of drought on the carbon balance in plants has gained great attention. Non-structural carbohydrate (NSC) dynamics have been suggested as an important trait reflecting carbon balance under drought conditions. However, NSC dynamics under drought and the response mechanisms of NSC to drought remain unclear, especially in water-limited savanna ecosystems. A precipitation exclusion experiment was performed to simulate different drought intensities in a savanna ecosystem in Yuanjiang valley in southwestern China. Growth, total NSC concentration and diurnal change of NSC were determined for the leaves and non-photosynthetic organs of three dominant species (Lannea coromandelica, Polyalthia cerasoides and Heteropogon contortus) throughout the growing season. Drought significantly reduced the growth of all the three species. Total NSC concentration averaged ~8.1%, varying with species, organ and sampling period, and did not significantly decrease under drought stress. By contrast, the diurnal change of NSC in these three species increased under drought stress. These results indicate that these three dominant species did not undergo carbon limitation. Thus, relative change in NSC is a more sensitive and effective indicator than carbon reserves in evaluation of plant carbon balance. These findings provide new insights for the understanding of carbon balance and the mechanisms of carbon starvation.