The microscopic structures of cross-linked natural rubber (NR) were investigated by means of contrast-variation small-angle neutron scattering (CV-SANS) coupled with "visualization-by-swelling method" as a function of dicumyl peroxide (DCP; cross-linker) content. where the various types of inhomogeneities in the rubber were visualized by swelling with deuterated solvent. Detailed analyses of the partial scattering functions of each component confirm the existence of network inhomogeneities due to cluster-like structures of polyisoprene chains as well as larger inhomogeneities of protein aggregates. The observed partial scattering functions of polyisoprene with different DCP contents clearly exhibited that (1) the network inhomogeneities were strongly suppressed by DCP addition and (2) the structure of protein aggregates was not significantly influenced by the introduction of the peroxide cross-linking. These nanoscopic structural aspects with respect to the content of cross-linker provide better understanding of the elastic properties of NR.