The invention provides freeze-thaw-resistant waterborne epoxy mortar and a preparation method thereof. The freeze-thaw-resistant waterborne epoxy mortar comprises 10 parts of epoxy resin, and every 10parts of epoxy resin correspondingly comprises 10-20 parts of waterborne curing agent, 0.1-3.0 parts of diluent, 0.1-0.5 part of defoaming agent, 0.1-1 part of accelerant, 20-300 parts of quartz sand, 1-30 parts of silica fume and 1-20 parts of water. The freeze-thaw-resistant waterborne epoxy mortar and the preparation method thereof have the advantages that compared with oily epoxy mortar and waterborne emulsion epoxy mortar, the waterborne epoxy mortar is moderate in solid content, high in curing rate, good in anti-vibration performance and very suitable for repair of high-speed rail baseplates; besides, compared with non-round-grain quartz sand, the adopted round-grain quartz sand has a smaller specific surface area and better workability.