The distribution of nanodiamond inside a nanomatrix, which is related to the mechanical and viscoelastic properties, is investigated for a natural rubber-nanodiamond composite. The composite is prepared by reacting nanodiamond with deproteinized natural rubber (NR-ND) in the presence of a tert-butylhydroperoxide (TBHPO)/tetraethylenepentamine (TEPA) radical initiator at 30 °C in the latex stage and subsequent drying. The morphology of the composite is observed by three-dimensional transmission electron microscopy. NR-ND prepared with an initiator exhibits a nanomatrix structure, whereas NR-ND prepared without an initiator displays an island matrix structure. The nanomatrix is densely loaded with 15 nm or smaller-sized nanodiamond. Both the mechanical and viscoelastic properties of NR-ND depend upon the morphology. The stress at break and the plateau modulus are 12 MPa and 1.19 × 106 Pa, respectively, when NR-ND is prepared with a TBHPO/TEPA initiator and contains 25 w/w % nanodiamond, which are 4 and 8 times higher than those of deproteinized natural rubber, respectively.