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, the salt tolerance of a coastal ecotype from Zhuhai and a terrestrial ecotype from Guangzhou were compared under salt stress. The morphological, physiological, and biochemical parameters related to growth, ion homeostasis, photosynthetic pigments, chlorophyll fluorescence parameters, oxidative stress, and apoptosis were measured in both ecotypes. Monitoring apoptosis showed that the protoplasts of the coastal ecotype underwent apoptosis and were later compared with those of the terrestrial ecotype. The coastal ecotype was also found to have higher regenerated stems; less water loss, sodium (Na+) uptake, and membrane damage; higher salt gland density and area; and better photosynthetic performance than the terrestrial ecotype. The coastal ecotype probably prevented salt-related damage by reducing its water loss and secreting excess Na+ through its lower stomatal density and higher density and area of salt glands. The coastal ecotype also maintained a better balance of Na+, potassium ions, nitrogen, and phosphorus under salt stress. Moreover, the coastal ecotype had higher activities of antioxidant enzymes, including superoxide dismutase, peroxidase, and catalase, and a higher content of non-enzymatic antioxidants, including proline and anthocyanins, which indicate a stronger antioxidant ability. Our results suggest that the coastal ecotype adapts to a higher salt tolerance than the terrestrial ecotype by enhancing its exclusion of salt, adjusting its osmolytes, and through photosynthetic efficiency, which could explain its successful invasion in the mangrove wetland ecosystem.