Polyacrylate/ZnO nanorods core-shell emulsion was prepared via emulsion polymerization for the first time. The distribution of ZnO nanorods in and out of the polyacrylate latex was achieved by adjusting the mass ratio of the non-ionic and anionic surfactants. The effects of surfactant composition on the distribution of ZnO nanorods in and out of polyacrylate latex, and the effect of composite latex microstructure on the properties of composite films were investigated in detail. The results showed that when the mass ratio of non-ionic and anionic surfactants was 0:1, the ZnO nanorods were located outside of the polyacrylate latex through electrostatic interaction with only anionic surfactants, forming polyacrylate@ZnO latex. Moreover, the ZnO nanorods can be uniformly dispersed in the composite film, and the tensile strength of the composite film was optimal. When the mass ratio of non-ionic and anionic surfactants was 1.5:1, all ZnO nanorods were encapsulated inside the polyacrylate latex to form ZnO@polyacrylate latex, the elongation at break and water resistance of the composite film were the best. When the mass ratio of non-ionic and anionic surfactants was 2:1, the agglomeration of ZnO nanorods in the composite film resulted in an increase in free volume, and the water vapor permeability of the composite film was optimal. Therefore, the microstructure of the hybrid latex can affect the macroscopic properties of the composite film. This study is expected to provide a theoretical basis for the structural design and performance optimization of the nanocomposite.