Wax coating is a widely used method to delay fruit maturation, especially for postharvest citrus fruit. Although treatment of citrus fruits with wax delays the color change process, the underlying mechanism is poorly understood. This study investigated the effect of SP-1 commercial wax on the peel coloration of postharvest Miyagawa Wase (Citrus unshiu Marc.) fruit. Results showed that wax treatment retarded the coloration of citrus fruit. Transcriptomic analysis revealed that multiple genes involved in cell wall, photosynthetic light reaction, lipid metabolism, primary metabolism and secondary metabolisms were differentially expressed after wax treatment. Specifically, genes involved in carotenoid biosynthesis including phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), lycopene β-cyclase (LCYb), β-carotene hydroxylase (CHY), violaxanthin de-epoxidase (VDE), xanthoxin dehydrogenase (ABA2) and 9-cis-epoxycarotenoid dioxygenase (NCED) were all down-regulated after wax treatment. Correspondingly, the contents of total carotenoid, violaxanthin (two isomers, tran- and cis-), β, β-xanthophylls (β-cryptoxanthin and antheraxanthin), luteoxanthin, lutein and abscisic acid (ABA) in wax-treated peels were all decreased. Collectively, our results suggest that SP-1 commercial wax can delay citrus fruit coloration by retarding the carotenoid biosynthetic pathway thus providing basis for future studies on the possible effects of waxing on the coloration of a wide range of fruits.