Disclosed is an amphiphilic multifunctional hybrid nanoparticle. The nanoparticle of the present invention has a detachable hydrophilic organic polymer with both a water-soluble long chain and a hydrophobic long hydrocarbon functional group attached to the surface, wherein the body of the nanoparticle is a silica or an organofunctional group substituted silica or an organofunctional group substituted silicon-oxygen bond network, and the nanoparticle contains a free organosiloxane with hydrophobic long hydrocarbon functional groups and a fatty acid or fatty acid ester or aluminum complex of fatty acid with hydrophobic long hydrocarbon functional groups. The nanoparticle can reduce the water permeability of the cement-based material; the cement-based material has the internal hydration products and interfaces are hydrophobized, further reducing the possibility that the harmful particles erode the cement-based material through moisture penetration; furthermore, Si—Al oxides participate is beneficial to the improvement of its mechanical properties.