Soil salinity is one of the most critical factors limiting plant growth and development. Carex leucochlora is an important turfgrass species with a wide distribution in northern China that is highly sensitive to salt stress, which impairs its development. Recently, melatonin has emerged as a nontoxic biomolecule that regulates growth and enhances salt tolerance in plants. In this study, the mechanism of melatonin’s regulation of plant growth and anatomical characteristics in C. leucochlora seedlings under continuous salt stress was explored. Our results indicated that salt stress strongly suppressed plant growth and leaf cell activity, inhibited root morphology and root activity, and negatively affected leaf and root anatomic structures in the seedlings. Conversely, melatonin (150 μmol L−1) pretreatment improved the detrimental effect of salt stress by restoring the morphology of the leaf, alleviating damage to the cell membrane, improving root activity, and altering the root architecture and plant growth attributes. Moreover, after 12 days of salt stress, anatomical observations of the leaf showed that the thickness of the leaf blade, vascular bundle area of the leaf main vein, vesicular cell area, thickness of the upper epidermis, and thickness of the lower epidermis were increased by 30.55, 15.63, 12.60, 16.76 and 27.53%, respectively, with melatonin under salinity. Melatonin treatment also showed an increase of 5.91, 7.59, 15.57, and 20.51% in epidermal thickness, vascular cylinder diameter, xylem vessel diameter, and pith cell diameter, respectively, compared with salt stress after 12 days. These results suggest that melatonin alleviated salt stress through augmenting seedling growth, leaf cell activity, and root characteristics, maintained the stability of anatomic traits to maintain chloroplast cell homeostasis, and also protected the vascular tissues to promote the radial transport of water and ions in the C. leucochlora seedlings. These modifications induced by the exogenous application of melatonin may help C. leucochlora to acclimate successfully to saline soils.