The invention discloses nano-silica modified geopolymer anticorrosive mortar and a preparation method thereof. The anticorrosive mortar comprises the following components: fly ash, metakaolin, modified sodium water glass, nano silica, a water-borne epoxy resin emulsion, a water-borne epoxy curing agent, hard basalt staple fibers, polyvinyl alcohol fibers, a polycarboxylate superplasticizer, an expanding agent, quartz sand and water. The nano-silica modified geopolymer anticorrosive mortar and the preparation method thereof provided by the invention have the performance characteristics of water resistance, permeability resistance, high strength, crack resistance, acid resistance, salt and alkali corrosion resistance, high cohesiveness and the like; and the nano-silica modified geopolymer anticorrosive mortar can be used for waterproof, crack-resistant and corrosion-resistant hydrological engineering such as foundation engineering facades in saline-alkali areas, piers and dams, ports and piers, building outer walls and roofs in acid rain areas and the like.