Root rot is a soil-borne disease primarily caused by fungi. The malady not only decrease the ability of absorbing water and nutrients, but also severely threat agricultural productivity. Recently, a new family member of two-dimensional (2D) transition metal carbide materials, MXene (Ti3C2Tx), has gained much interest as a promising approach to control fungi. However, the efficient use and mechanism of MXene in protecting plant against pathogenic fungus are still rarely reported. Here, the synthesized MXene were first characterized by the atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic light scattering (DLS), transmission electron microscopy (TEM) and X-ray photoelectron spectra (XPS). MXene application in soil obviously enhanced the root rot disease resistance of T. grandis. Soil microbial community analysis indicated that the abundance of Fusasium genus was decreased by 68.32% after MXene treatment. Further, MXene specially affected the permeability of Fusarium solani via damaging their cell membranes, thereby causing the disintegration and cell death of F. solani. In addition, MXene nanoflakes could transport into roots through T. grandis root air space, which resulted in the accumulation of lignin in roots via enhancing the expression and activities of lignin biosynthesis-related genes in T. grandis roots. Taken together, our finding pioneers comprehensive insights into the antifungal mechanism of MXene against F. solani and the efficiency use of MXene in protecting plant against pathogenic fungus, which will prompt the rapid development of nanotechnology in sustainable forestry.