Effect of proteins, constituents of the island-nanomatrix structure, on dispersion of zinc to natural rubber was investigated by transmission electron microscopy-energy dispersive X-ray spectroscopy (TEM-EDX) and focused ion beam-scanning electron microscopy-energy dispersive X-ray spectroscopy (FIB-SEM-EDX). Films of natural rubber and deproteinized natural rubber (DPNR) prepared with urea were embedded in a mixture of ZnO, vulcanization accelerator and sulfur, and they were heated at 150 °C for 5 h. Migration of Zn from surface to inside of the films was observed by FIB-SEM-EDX. The Zn migrated from the surface to 14 μm for natural rubber, but not for DPNR. The optimum vulcanization time for natural rubber was short, i.e., about 4 min, whereas it was long for DPNR, i.e., about 15 min. To confirm the effect of the proteins, a latex-mixed rubber compound was prepared by mixing the latex with sulfur, ZnO and vulcanization accelerator followed by drying with a hotplate at 150 °C for 45 s since the proteins are segregated on the surface of natural rubber particles in the latex stage. Vulcanization was accelerated for the latex-mixed natural rubber compared with mechanically mixed natural rubber compound that was prepared by mixing natural rubber with ZnO, vulcanization accelerator and sulfur with a two-roll mill. The resulting latex-mixed natural rubber vulcanizate was superior in mechanical properties to the mechanically mixed natural rubber vulcanizate. It was found by rubber-state NMR spectroscopy that the difference in mechanical properties was attributed to the difference in the cis-1,4-average sequence length of the vulcanizates, which came from the difference in the dispersion of Zn.