Abstract The cuticle wax coating the primary aerial organs of terrestrial plants consists of epicuticular and intracuticular wax; this wax protects the plants and affects many physiological characteristics. The glossy, bright green BianGan Welsh onion (Allium fistulosum L.) (GLBG) was derived from a natural variation in the field, and it was tentatively demonstrated that the GLBG or glossy phenotype is conditioned by a single recessive gene. An analysis of the physiological characteristics related to cuticle wax showed that the density and shape of wax crystals on the leaf surface of GLBG clearly differed from those of the waxy BianGan Welsh onion (BG) and that its epicuticular wax coverage was 50% less than that of BG. However, there were no significant differences in cuticle membrane permeability or stomatal density, indicating similar drought resistance abilities. Compared to BG, GLBG had poorer growth but higher net photosynthetic rate and carotenoid content. Our research on wax-related genetic identification and the analysis of GLBG physiological characteristics provides a reference for the further exploration of genes related to cuticle wax biosynthesis and secretion in Welsh onion and for potential applications in Welsh onion breeding.