The invention provides a ballastless track packing layer healant and a preparation method thereof. The healant is prepared from the following raw material components in percentage by weight: 10 to 20 percent of toluene diisocynate (TDI) prepolymer, 70 to 80 percent of ether polymer and 8 to 12 percent of modifier. The healant is prepared by mixing the raw materials according to a formula ratio ina reaction kettle to react the raw materials at a certain temperature. The healant provided by the invention has high bonding force and stress coordinating performance for a ballastless track packinglayer, can reach a traffic intensity in short time period at normal temperature, has high filling operability, can be used for a long time, is very durable, can relieve train load, vibration and shock, avoids hardening and contracting and can be manufactured simply.