Epicuticular waxes form the outermost layer over the membrane and are visible on Arabidopsis inflorescence stem surfaces as a bluish-white colored coating. In the current study, the effects of Sclerotinia sclerotiorum on epicuticular wax morphology and constituents in Arabidopsis thaliana stems were analyzed, aiming to elucidate the relationship between fungal invasion and plant epicuticular wax. Wax mutants cer1 (the contents of alkanes, secondary alcohols, and ketones reduced significantly), cer4 (the contents of primary alcohols reduced significantly), and one wild type of A. thaliana were selected as experimental materials. Scanning electron microscope technology was used to investigate the changes of crystalloid structure. Gas chromatography and mass spectrometry technology was used to measure the amounts of total wax and wax constituents. The results showed that wax morphology of A. thaliana wild type was composed primarily of vertical rods and plates, that of wax mutant cer1 was composed primarily of horizontal needles and plates and the density and size of crystalloids reduced. Wax mutant cer4 had a very high density of vertically oriented (relative to the horizontal cuticle surface) plate-like waxes. The infection of S. sclerotiorum altered the crystalloid morphology of epicuticular wax in stems. The changing pattern of wax crystalloid morphology under S. sclerotiorum infection might be as follows, decrease of "rod crystalloids-fusion of wax crystalloids into epidermis-surface protuberances-epidermis cracks. These changes of wax crystalloid morphology enabled S. sclerotiorum break through the cuticle barrier and infect plant. Infection also altered the secretion amounts of wax constituents. After inoculation with S. sclerotiorum, the content of primary alcohols in wild type and wax mutants increased significantly except cer1, while the content of alkanes, secondary alcohols, ketones and total wax decreased significantly. This suggested that more wax precursors converted to primary alcohol from acyl reduction pathway under S. sclerotiorum stress, resulting a decrease of wax amounts from decarbonylation pathway. The S. sclerotiorum promoted it's penetration to epidermis by altering the crystalloid morphology and constituents of plant epicuticular wax.