The invention discloses a hollow polymer emulsion and a preparation method thereof. The preparation method adopts the processes of emulsion polymerization, core-shell emulsion polymerization and the like to prepare the hollow polymer emulsion. An emulsion particle is of a structure with a hard shell and a soft shell, and the void fraction of a film formed by the emulsion reaches more than 50 percent. A variety of unsaturated monomers, emulsifier and initiator are adopted to prepare the hollow polymer emulsion, in particular, isobornyl methacrylate and 2,2,3,4,4,4-hexafluorobutyl acrylate are chosen as shell monomers, the contents of isobornyl methacrylate and 2,2,3,4,4,4-hexafluorobutyl acrylate respectively account for 2 to 5 percent and 3 to 6 percent by weight of the total amount of the emulsion, and the mechanical properties, the weather fastness and the dirt resistance of the emulsion film are effectively enhanced. The product has an excellent dry hiding effect, can decrease the density of the film and improve handle, and can be applied in the fields of water-borne coating, paper coating, industrial coating, ink and the like.