The chemical composition and structure of the cuticular wax in blue honeysuckle fruit were investigated using gas chromatography–mass spectrometry (GC–MS) and scanning electron microscopy (SEM). The results revealed that the cuticular wax was dense and uniform, taking on a tubular form. A total of 158 wax components were identified, including alkanes, terpenes, ketones, alcohols, fatty acids, and esters. The wax was found to be particularly rich in alkanes. After storage, the wax content decreased, whereas an increase in 1-undecanol. The destruction or reduction of cuticular wax resulted in a more rapid decline in storage quality, loss of nutrients, and a decrease in antioxidant phytochemicals. Meanwhile, wax metabolizing enzyme activity and gene expression increased. This study presents a deeper understanding of blue honeysuckle fruit cuticular wax composition and aids to developing effective measures to delay its postharvest fruit quality deterioration.