The invention relates to a high-elasticity anti-seepage filling material and an anti-seepage method for a caulking of a concrete member expansion joint. The high-elasticity anti-seepage filling material comprises mortar and a compound fiber material mixed with mortar, wherein the mortar comprises the following raw materials, by weight part, 20-35% of single-component polyurea, 64.7-78.25% of sand aggregate, 0.2-1.05% of a mixed liquid of butanone and water, and 0.1-0.7% of a thixotropic agent. The high-elasticity anti-seepage filling material is good in caking property and is superior to a polysulfide sealant and a polyurethane caulking material. The high-elasticity anti-seepage filling material has high strength and certain elasticity, is excellent in abrasion-resistant and impact-resistant effect, and is quite suitable for repairing a defect part of a concrete expansion joint of a flood releasing structure. The anti-seepage filling material is good in elasticity, and the caulking material can recover to the original shape after being compacted to 50%. The anti-seepage filling material has low-temperature flexibility and is suitable for application to the northern severe cold region. The high-elasticity anti-seepage filling material is excellent in aging resistance and can resist a water pressure of 0.55 MPa without deformation.