Waterlogging caused by rainfall or improper irrigation is a serious threat that limits the growth and yield of crop plants by hypoxia stress. In the current study, the seedlings of vegetable sweet potato (Ipomoea batatas (L.) Lam.) variety ‘NC1’ (hypoxia-tolerant) and ‘C211’ (hypoxia-sensitive) were treated with oxygen content of 2 mg/L. It was found that the growth rate, net photosynthetic rate (P_N), transpiration rate (E), stomatal limitation (L_s), maximum net photosynthetic rate (A_max), diurnal respiratory rate (R_d), maximum Rubisco carboxylation rate (Vc_max), maximum electron transport rate (J_max), ABA (abscisic acid) and IAA (indole-3-acetic acid) content were significantly higher in ‘NC1’ than those of ‘C211’. It is concluded that under hypoxia stress, tolerant genotype could maintain higher photosynthetic efficiency by maintaining higher stomatal conductance and Rubisco efficiency, to maintain the growth of the root system and the canopy. This study provides the basis for further dissection of the mechanism of low-oxygen stress in sweet potato.