The addition of surface functional groups to multi-walled carbon nanotubes (MWCNTs) expands their application in engineering, materials, and life science. In the study, we explored the antifungal activities of MWCNTs with different surface groups against an important plant pathogenic fungi Fusarium graminearum. All of the OH-, COOH-, and NH 2-modified MWCNTs showed enhanced inhibition in spore elongation and germination than the pristine MWCNTs. The length of spores decreased by almost a half from 54.5 μm to 28.3, 27.4, and 29.5 μm, after being treated with 500 μg·mL −1 MWCNTs-COOH, MWCNTs-OH, and MWCNTs-NH 2 separately. Furthermore, the spore germination was remarkably inhibited by surface-modified MWCNTs, and the germination rate was only about 18.2%, three times lower than pristine MWCNTs. The possible antifungal mechanism of MWCNTs is also discussed. Given the superior antifungal activity of surface modified MWCNTs and the fact that MWCNTs can be mass-produced with facile surface modification at low cost, it is expected that this carbon nanomaterial may find important applications in plant protection.