A polyurethane caulking material for expansion joints of a ballastless track of a high speed railway is disclosed. The caulking material is prepared from two parts A and B. the part A is composed of the following raw materials, by weight, 100 parts of isocyanate and its prepolymer, 10-150 parts of a plasticizer, 5-150 parts of a solid filler, 1-20 parts of a diluents, 1-5 parts of an adhesion promoter, 0-10 parts of a thixotropic agent and 1-3 parts of a water-removal agent. The part B is composed of the following raw materials, by weight, 10-20 parts of modified polyhydric alcohol, 1-5 parts of a diluent, 2-30 parts of a plasticizer, 5-30 parts of a solid filler, 0-5 parts of a thixotropic agent, 0.5-2 parts of an antifoaming agent, 0.1-1 part of an anti-aging agent and 0-0.01 part of a catalyst. The mass ratio of the part A to the part B is 4:1-10:1. The polyurethane caulking material has advantages of good low-temperature curing performance, high displacement capability, low tensile modulus, good bond property and excellent endurance quality and fatigue resistance, and is suitable for expansion joints of a ballastless track of a high speed railway as well as expansion joints of roads and airfield runways.