The invention provides a water-borne epoxy resin modified cement mortar repair material and a preparation method thereof. According to the formula composition, the water-borne epoxy resin modified cement mortar repair material comprises materials in percentage by weight as follows: 27%-30% of cement, 56%-59% of sand, 0.8%-1.0% of an expanding agent, 0.5%-0.7% of silica fume, 5.0%-7.5% of water, 2.0%-5.0% of water-borne epoxy resin, 1.0%-2.5% of a curing agent, 0.19%-0.22% of an antifoaming agent and 0.14%-0.16% of a water reducing agent. The water-borne epoxy resin modified cement mortar repair material has the characteristics of short setting time, excellent fluidity, high anti-compression and anti-bending strength, seismic resistance, low shrinkage strain, good durability, good water resistance, simplicity in production, convenience in construction and the like, the particularly prominent properties include the ultrahigh bonding strength and the excellent durability, the bonding strength is 100%-200% higher than that of general modified cement mortar, and the cement mortar repair material can be suitable for repairing cracks of concrete structures and is particularly applicable to structural engineering such as a subway, a bridge, an airport runway, an aqueduct, a tunnel lining and the like with higher repair difficulties.