The invention provides a preparation method of a graphene functionalized silicon-based probe. According to the graphene functionalized silicon-based probe provided by the invention, the ionic liquid is adopted to perform carbonization pretreatment on the probe sample, and the carbon layer plated on the surface of the probe in advance is utilized to protect the silicon-based probe tip, so that the reaction between the metal coating and the silicon-based probe is effectively avoided in the high-temperature quenching process of graphene growth; therefore, graphene successfully grows on the surface of the probe, the appearance of the tip of the probe is maintained, the surface of the tip is flat, and the diameter of the tip is nano-sized. The graphene functionalized silicon-based probe prepared by the method has excellent tip sharpness, conductivity and oxidation resistance.