Cold storage of fruits is the best strategy to extend shelf life. However, storage temperature below 8°C mostly causes chilling injury (CI). Thus, exogenous melatonin treatment is an alternative safe preservative to alleviate CI and induce cold tolerance in postharvest of fruits and vegetables. This paper reviewed the recent progresses of melatonin-mediated physiological, biochemical and molecular mechanisms on chilling tolerance of fruits and vegetables. Among cold tolerance mechanisms, melatonin substantially enhances enzymatic and non-enzymatic antioxidants removing reactive oxygen species (ROS). Melatonin triggered phenol accumulation which associated with 2,2-diphenyl-1picryl hydrazyl (DPPH) scavenging capacity and reduction of oxidative damage. In addition, melatonin extensively maintained intracellular energy and enhanced energy regulation associated enzymes, thereby maintaining cellular stability. Melatonin induces unsaturated/saturated fatty acid (unSFA/SFA) ratio, improving cellular fluidity. Besides, melatonin regulates arginine metabolisms via increased polyamines, proline and γ-aminobutyric acid (GABA) contents. Furthermore, melatonin possibly encodes calcium-dependent protein kinases (CDPK) and mitogen-activated protein kinases (MAPK) cascades. Moreover, it substantially induces Ca2+ signaling transduction pathways. As part of the signaling pathway, melatonin activates C-repeat binding factors (CBFs) as transcriptional factors for cold acclimation. Therefore, this review concluded that exogenous melatonin improves chilling stress tolerance by coordinating biochemical and molecular mechanisms at post-harvest life of fruits and vegetables and extending shelf life.