The invention relates to a material with metal silicide nanometer structure and the preparation method thereof. The material comprises a metal silicide nanometer structure which is produced on an SOI substrate; the thickness of an insulation medium layer of the SOI substrate is 100 to 1000 nanometers, and the thickness of silicon thin film is 50 to 500 nanometers. The preparation method comprises the following steps: a required mask feature structure of nanometer structure is produced on the silicon thin film surface of the SOI substrate after cleaning, drying, spin coating positive photoresist, exposing, developing, and fixing; the silicon thin film of the SOI substrate is etched to the required nanometer structure by adopting a reactive ion etching, the etching depth is equal to the thickness of the silicon thin film, a metal thin film which is required by the metal silicide is deposited on the isolation layer which contains the silicon nanometer structure, then high temperatures anneal is performed to ensure that soild phase reaction is reacted between the metal and the silicon, thus to generate the metal silicide, the unreacted metal is removed through chemical etch, and then the metal silicide nanometer structure is formed. The method is simple, and the position and the dimension of the nanometer structure can be controlled.