In order to reveal the characteristics of resistance to apple scab at the level of histocytology, the changes of leaf tissue and cell structure of apple resistant cultivar “Qinguan” and susceptible cultivar “Gala” were systematically observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) after inoculating the hosts with conidial suspension of Venturia inaequalis. The results of SEM observation showed that hypha of pathogen grew and expanded along the veins of host leaf in 48 hours after inoculation, and invaded into leaf tissue directly or from stomata. TEM observation showed that the leaf cuticle thickness of “Qinguan” was significantly thicker than that of “Gala”, and the average cuticle thickness of “Qinguan” was 1.75 μm while that of “Gala” was 1.06 μm. It was observed that the hyphae of Venturia inaequalis expanded intercellularly in the mesophyll resulting in palisade cells shrank, loosely arranged, decreased in number, and the chloroplasts were deformed and thereby seriously damaged the cultivar “Gala”. Large starch granules appeared and intracellular substances leaked out, resulting in seriously cell necrosis in the later stage. A similar phenomenon also occurred in “Qinguan”, but the degree of cells damage was obviously alleviated. The research results indicated the cultivar “Qinguan” was able to resist to pathogen’s penetration and extension and delay the development of scab pathogenesis, and hopefully can be used as scab-resistant breeding material.