Previously, we obtained a wax-deficient mutant 'Ganqi 3' (MT) from 'Newhall' navel orange (Citrus sinensis [L.] Osbeck cv. Newhall, WT). The weight loss and postharvest decay in MT fruit were much higher than those in WT fruit after long-term cold storage. To understand the underlying mechanism, the changes in the morphology, chemical composition and gene expression of cuticular waxes between WT and MT fruit were compared during 150 days of storage at 4 °C. The density of epicuticular wax crystals and the contents of most of the aliphatic wax fractions in MT fruit were much lower than those in WT fruit over 90 days of storage. Further research revealed that the differences in the morphology and chemical composition of cuticular waxes might be important causes for the differences of postharvest weight loss and decay rates between WT and MT fruit. Notably, the expression profiles of 16 wax-related genes in WT and MT fruit were consistent with the change trends of corresponding cuticular wax components during cold storage. These results suggest that the morphology and chemical composition of cuticular waxes may be regulated by wax-related genes and play an important role in regulating the postharvest weight loss and the tolerances to postharvest decay in navel orange.