Fusarium wilt is one of the main diseases of sweet potato in south China. In this study, ultrastructure was performed to understand the disease-resistant mechanism of cell structure alternation in sweet potato via Fob (Fusarium oxysporum f. sp. batatas) inoculation treatment. Sweet potato cultivars with different disease-resistance [Highly resistant (HR) cultivars: Jinshan57, Moderate susceptibility (MS) cultivars: Reshu NO.1, Higher susceptible (HS) cultivars: Xinzhonghua,] were inoculated by stem base, and any alteration in cell structure of the sample was observed by direct observation combining with microscopy and transmission electron microscope(TEM) technology. The results showed that there were different performances among different cultivars after inoculation. The Fob mycelium growth was not observed in the stem of Jinshan 57 (the HR cultivars ) after inoculation, which cell structural integrity was not violated. With the inoculation of Fob, the cells in stem base of Reshu No.1 (MS cultivar) were violated to apoptosis. While in the middle part of which stem, the plant-pathogen interaction was more active and the transportation of plant nutrition was disrupted. The Fob mycelium spread from the stem base to the top stem through the vascular bundles. After inoculated by Fob, the mycelium spread to the epidermal cells, cortex and vascular bundles of Xinzhonghua (the HS cultivar ) from the injury, then spread to the middle and top part of the stem till the whole plant exsiccation. During this period, the thylose was observed in the vessels, and rupture of cell wall and membranes of cytoplasmic organoids were also observed. At the same time, the sediment of cell wall and tubercles emerged wherever the pathogen invasion, and the Fob hyphae were surrounded by a variety of amorpphis or cellosilk net.