The present study investigated the role of melatonin (MT) in improving the storage duration of cut chrysanthemum flowers. The flowers were exposed to different concentrations of MT and stored at 20°C ± 1°C and 90% relative humidity. Cut flowers treated with 5 µM MT had longer storage durations than those kept in water. The results demonstrated that 5 µM MT significantly enhanced the water balance and decreased water loss. The 5 µM MT treatment group exhibited a significantly higher fresh weight and flower diameter than the control group. Leaves of cut flowers treated with MT showed lower malondialdehyde (MDA) contents and lipoxygenase (LOX) activity levels than the control group. Moreover, the application of MT enhanced the antioxidant capacity of leaves by upregulating the activities of the key enzymes involved in scavenging reactive oxygen species, including superoxide dismutase, peroxidase, and catalase. This suggests that MT effectively mitigated oxidative stress and cell damage in the leaves during storage, which may contribute to its ability to extend the shelf life of cut flowers. Furthermore, 5 µM MT significantly reduced the proline content of the petals and leaves of treated flowers. These findings suggest that MT improves the storage duration most likely by regulating the antioxidant system and water balance of cut chrysanthemum flowers.