The origin of energetic elasticity in conjunction with the entropic elasticity for natural rubber with a nanodiamond nanomatrix structure was investigated in terms of bound rubber formed between nanodiamonds, based on the interaction between natural rubber and nanodiamonds inside the nanomatrix. The natural rubber with a nanodiamond nanomatrix structure was prepared by reacting nanodiamonds with deproteinized natural rubber in the presence of tert-butylhydroperoxide/tetraethylenepentamine at 30 °C in the latex stage followed by drying. Morphology of the products was observed by two-dimensional and three-dimensional transmission electron microscopies. The effect of bound rubber on the mechanical properties of the products was investigated by measurements of the dynamic mechanical properties and differential scanning calorimetry. The contribution of bound rubber was estimated by combining the Takayanagi equation and modified Guth–Gold equation. A significant increase in complex modulus was attributed to the effect of the bound rubber.