Ipomoea pes-caprae has potential ecological restoration value as a salt- and drought-tolerant pioneer plant, while fewer studies on its environmental and physiological adaptations in different habitats. Here, we selected I. pes-caprae populations from Sansha (coral soil, CS) and Huizhou (sandy soil, SS), measured key physiological and ecological characteristics, and explored the mechanism of its adaptation. The results showed that the leaf water content and the delta 13C of I. pes-caprae in the CS habitat were significantly lower than those in SS, indicating that it adapted to the arid environment by improving water use efficiency. The carbon and nitrogen contents of I. pes-caprae leaves in the SS habitat were significantly higher than CS, while phosphorous content was lower. I. pes-caprae leaves from the CS habitat had a higher soluble sugars and non-structural carbohydrates content, suggesting that they may enhance stress tolerance by accumulating osmoregulatory substances. Still, its higher malondialdehyde content and lower superoxide dismutase and glutathione activities indicated that it may be subjected to stronger oxidative stress. In contrast, I. pes-caprae from SS habitats exhibited a stronger antioxidant system. I. pes-caprae in the CS habitat had lower chlorophyll content and higher carotenoid accumulation, suggesting that they may reduce high light damage by lowering photosynthetic activity, whereas SS habitat had higher photosynthetic capacity. In summary, I. pes-caprae in CS habitats adapted to arid, infertile, and hypersaline environments mainly through water conservation, osmoregulation, and reduced photosynthetic activity, whereas SS habitats relied on higher nutrient utilization efficiencies, photosynthesis, and antioxidant systems to maintain rapid growth.