Removal of protein from natural rubber was carried out via deproteinization of natural rubber in the latex stage. Then, its effect on the molecular structure and properties of natural rubber was investigated. Urea, SDS, and acetone were used as denaturing agent, a surfactant, and a polar solvent in the deproteinization, respectively. Various deproteinized natural rubbers were obtained after one, two, and three times of centrifugation with and without acetone, namely DPNR1, DPNR2, DPNR3, DPNR1-A, DPNR2-A, and DPNR3-A. It was found that the total protein content significantly decreased as increasing the number of centrifugations; however, the total fatty acid contents showed a slight decrease. Structural characteristics analyzed by nuclear magnetic resonance spectroscopy indicated no changes in the chemical structure of natural rubber after deproteinization. However, the removal of proteins significantly enhanced the resolution of the NMR signals. Gel content and tensile properties of natural rubber showed a decrease in the removal of proteins, which was associated with the decrease in the number of the inherent branching points formed in natural rubber.