The invention relates to a silicone caulking material for concrete expansion joints of ballastless tracks and a preparation method thereof. The caulking material is composed of the following raw materials in parts by mass: 100 parts of alpha, omega-dihydroxy polydimethylsiloxane, 10-35 parts of a plasticizer, 70-120 parts of filler, 0.5-10 parts of a thixotropic agent, 6-12 parts of a crosslinking agent, 1-8 parts of a chain extender, 0.3-3 parts of an adhesion promoter, 0.1-2 parts of a catalyst, 0.005-0.5 part of a pigment, 0.5-5 parts of a storage stabilizer, and 1-3 parts of a deep curing agent. The silicone caulking material is prepared by using the preparation method disclosed by the invention. The silicone caulking material has the characteristics of good construction performance, high displacement capacity, good interface adhesion, excellent aging resistance, long storage life, good deep-layer curing performance, and the like, is suitable for being applied to concrete expansion joints of ballastless tracks of high-speed rails, expansion joints of airport pavements and cement concrete pavements, and the like, and also can be applied to the failure repair of existing expansion caulking materials.