Longkong (Aglaia dookkoo Griff.) fruit is prone to rapid pericarp browning and shortened shelf life (<7 days) under prolonged low-temperature storage. This study investigates the effect of an edible coating, comprising carboxymethyl cellulose (CMC) and gelatin in a fixed 3:1 ratio, integrated with various concentrations of melatonin (MT) (0.4, 0.8, and 1.2 mM/L) to mitigate chilling injury in longkong fruit. Coated longkong fruits were stored at 13 °C with 90% relative humidity for 18 days and underwent physicochemical evaluations every three days. Samples coated with CMC-Gel without MT and uncoated fruits were served as controls. The findings indicated that the CMC-Gel-MT coating significantly mitigated pericarp browning, chilling injury, weight loss, and respiration rate increase under extended cold storage conditions. High concentrations of MT (≥0.8 mM/L) in the coating notably inhibited the activities of cellular degrading enzymes such as lipoxygenase and phospholipase D. This inhibition contributed to reduced membrane permeability, lower reactive oxygen species accumulation (H2O2, OH−, O2−), and decreased malondialdehyde levels in the longkong pericarp. Furthermore, the CMC-Gel-MT coating increased the activity of phenylalanine ammonia lyase, leading to an enhancement in phenolic content. Consequently, it improved the fruit’s ability to scavenge DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS (2,20-azino-di-3-ethylbenzthiazoline sulfonic acid) radicals. Control samples exhibited high levels of pericarp browning-related enzymes (polyphenol oxidase, peroxidase), whereas CMC-Gel-MT-coated fruits, particularly at higher MT concentrations, showed significant reductions in those enzyme activities. In conclusion, incorporating high concentrations of MT in a CMC-Gel-based edible coating is a promising alternative for mitigating chilling injury in longkong fruit.