Fusarium graminearum is an important causal agent of maize seedling blight. The species includes several chemotypes that produce various forms of deoxynivalenol (DON) and nivalenol (NIV). To understand the effects and roles of F. graminearum mycotoxins on maize seedling blight occurring at Zhang Ye of Gansu, China, 23 isolates of F. graminearum were collected and characterized. A PCR assay showed all 23 isolates belonged to the 15-acetyldeoxynivalenol (15-ADON) genotype. This was also confirmed by production of both DON and 15-ADON in either rice culture medium or maize seedling roots, detected by high performance liquid chromatography and mass spectrometry. In maize seedling roots, 15-ADON dominated at 6 days post inoculation (dpi) and DON was the main mycotoxin at 12 dpi. The biomass of F. graminearum doubled from 6 to 12 dpi, and was positively correlated with virulence of the isolates. Both mycotoxins affected maize root vitality, but 15-ADON had a greater effect than DON. ALDH9 and MDH, two dehydrogenase synthesis genes in maize, showed a lower relative expression in 15-ADON treatments than in DON treatments. It indicated that both mycotoxins affected seed germination and root development, with 15-ADON being more destructive. Under scanning electron microscopy and transmission electron microscopy, root hair formation and development were delayed by DON, but completely inhibited by 15-ADON. 15-ADON caused cell shrinkage, loose cellular structure, and widened intercellular spaces; it also destroyed organelles and caused plasmolysis, and eventually ruptured cell membranes causing cell death. DON did not affect cell morphology and arrangement, but altered the morphology of organelles, forming concentric membranous bodies and a large amount of irregular lipid droplets. Thus, both mycotoxins contributed to symptom expression of maize seedling blight, but 15-ADON was more destructive than DON.