A pot experiment was conducted to study the variation of water use efficiency (WUE) and carbon isotope discrimination in maize under water deficit conditions and their relationship. Three water regimes were imposed and they took up the fraction of field capacity of the soil were: 50% (W1), 75% (W2), 100% (W3). The results showed that the biomass of various organs of sweet potato increased with moisture increases, and reaching the maximum in the 100% of field capacity (W3). WUE under 50% of field capacity (50%) was highest. However, the high moisture treatment reduced the proportion of the photo-assimilates distributed to the underground; meanwhile, photosynthetic rate positively correlated with RuBisCO activity; Δ13C of different organs of sweet potato were different during different growth stages under the three water treatments. Δ13C in root was the smallest, and then followed by petioles, stems, leaves, indicating that the carbon isotope fractionation occurred when the photoassimilates distributed in various organs, D13C of various organs presented consistent negative correlation with WUE during different growth stages. In summary, the carbon isotopes can be used as a simple, quick and accurate method for evaluating WUE of sweet potato.