The purpose of this study was to investigate the effects of plant growth regulators (PGRs) on the growth of aboveground and underground parts, photosynthesis, stress physiology, and storage roots in sweet potato. Controlled field experiments were conducted using Yuhongxinshu 98 as the experimental material. Seven treatments were applied: normal soil moisture (CK), early-stage drought stress (D), early-stage drought stress+6-BA (D1), late-stage waterlogging stress (W), late-stage waterlogging stress + uniconazole (W1), DW, and D1W1. We investigated the effects of these two stresses and analyzed the roles of PGRs in yield and quality, the growth of the main vine and underground parts, photosynthetic characteristics, osmotic adjustment substances, and the activities of stress-related enzymes. The results showed that: (1) the three types of water stress, namely D, W, and DW, caused substantial reductions in sweet potato yield, by 55.65%, 35.62%, and 54.20%, respectively. After exogenous application of PGRs, the yields of D1, W1, and D1W1 increased by 45.14%, 48.84%, and 58.10%, respectively, compared with those of D, W, and DW. (2) Water stress under D, W, and DW significantly decreased the contents of starch, soluble protein, and soluble sugar in the storage roots of sweet potato, and spraying 6-BA and uniconazole effectively improved these quality traits. (3) D1 and W1 were beneficial to main vine thickening in sweet potato. W1 significantly inhibited the elongation of the main vine, and its ratio of root-to-shoot (R/T) was significantly higher than that of W. (4) The net photosynthetic rate (Pn) was inhibited by treatment D, which resulted in a hysteresis effect. Compared with CK, stomatal conductance (Gs) under D and W decreased by 21.92% and 19.05%, respectively. (5) Both D and D1 increased proline (Pro) and soluble protein contents in the leaves. (6) Both drought stress and waterlogging stress significantly enhanced catalase (CAT) activity. After spraying 6-BA and uniconazole, namely under D1 and W1, CAT activity remained higher than that in CK. In conclusion, whether as single drought stress, single waterlogging stress, or drought followed by waterlogging stress, all three stress conditions affected the normal growth and yield formation of sweet potato. After exposure to these stresses, spraying 6-BA under drought stress or uniconazole under waterlogging stress alleviated the negative effects, improved storage root quality and photosynthetic capacity, regulated the contents of osmotic adjustment substances, promoted the activities of stress-related enzymes, enhanced the adaptability of sweet potato to these two stresses, and reduced stress injury, ultimately increasing the yield and quality of storage roots under water stress.