Palmate-leaved morning glory (Ipomoea cairica (L.) Sweet) is a fast-growing perennial herbaceous twining vine that was recently discovered to invade mangrove wetlands in China. To understand the mechanism of its successful invasion, we compared the salt tolerance of a halophytic line from Zhuhai and a non-halophytic line from Guangzhou under salt stress. We measured morphological, physiological, and biochemical parameters related to growth, ion homeostasis, photosynthetic pigments, chlorophyll fluorescence parameters, oxidative stress, and apoptosis in both lines. Monitoring apoptosis showed that the halophytic line had a delayed protoplast apoptosis compared with the non-halophytic line. We also found that the halophytic line had higher stems that regenerated; lower water loss, Na+ uptake, and membrane damage; a higher density and area of salt glands; and better photosynthetic performance than the non-halophytic line. The halophyte prevented salt-related damage by reducing water loss and secreting excess sodium ions (Na+) through its lower stomatal density and higher density and area of salt glands. The halophytic line also maintained a better balance of Na+, potassium ions, nitrogen, and phosphorus under salt stress. The halophytic line had higher activities of antioxidant enzymes, including superoxide dismutase, peroxidase, and catalase, and non-enzymatic antioxidants of proline and anthocyanins, which indicate a stronger oxidative stress response. Our results suggest that the halophytic line adapts to higher salt tolerance than the non-halophytic line by enhancing its salt exclusion, osmolyte adjustment, and photosynthetic efficiency, which could explain its successful invasion in the mangrove wetland ecosystem.