The invention belongs to the technical field of pavement materials, and specifically discloses a negative thermal expansion modified asphalt caulking material and an application method thereof. The modified asphalt caulking material comprises the components in percentages by weight: 40-62% of base asphalt, 4-10% of negative thermal expansion materials, 3-5% of expansion coordination agents, 30-42% of filler and 1-3% of additives. The base asphalt is SBS modified asphalt, the negative thermal expansion materials are zinc cyanide, cadmium cyanide; the expansion coordination agent is zirconium phosphate sodium; the filler is calcium power, and the additives are sodium polyacrylate or polyoxyethylene polyoxypropylene copolymers. The caulking material disclosed by the invention can effectively control crack propagation caused by material thermal expansion and contraction, so that cracks in old cement concrete pavement can be effectively filled, so that the material plays a role of water resistsance, and the driving comfort can be improved. The caulking material disclosed by the invention can be popularized and applied in functional repair of old cement concrete pavement and building cracks filling engineering.