Protein effect on vulcanization of NR, obtained from Hevea brasiliensis, was investigated by analyzing the crosslinking structure of the resulting vulcanizates prepared from untreated NR, deproteinized natural rubber (DPNR), and protein-free natural rubber (PFNR) by swelling methods and rubber-state NMR spectroscopy. The proteins present in NR were removed by three methods: deproteinization with enzyme, urea, or urea–acetone in the presence of sodium dodecyl sulfate. The amount of proteins present in NR, approximately 0.238 w/w%, was reduced to 0.000 w/w% by urea–acetone deproteinization, whereas it was reduced to approximately 0.003 and 0.019 w/w% by enzyme and urea deproteinizations, respectively. Hardness, swelling degree, and crosslinking structure depended on the amount of proteins. Changes in mechanical properties for the vulcanizates prepared from not only non-filler compounds but also carbon black–filled and silica-filled compounds were attributed to the amount of proteins.