Imaging of latex particles, especially those with low glass transition temperature (Tg) has been a challenging issue. Different sample preparation methods for characterization of the morphology of a poly(n-butyl acrylate)/polystyrene two-phase latex are discussed and compared in this study. A method via hydroxyethyl cellulose embedding combined with ruthenium tetraoxide (RuO4) staining for scanning transmission electron microscope (STEM) observation is developed. By using this method, the spherical shape of latex particles can be maintained without deformation. The degree of incorporation of RuO4 into latex particles and cellulose matrix is different, which makes latex particles readily identifiable from cellulose matrix under STEM. A series of latexes with different structures such as copolymer latex and organic-inorganic hybrid latex were also successfully investigated by this method. The results indicate this specimen preparation method can be applied to study the morphology of a wide range of latex systems.