The inclusion of highly anisotropic clay nanoparticles (nanoclays) in cross-linked natural rubber (NR) provides a more homogeneous distributed network structure and induces an early onset as well as enhancement of crystallization under uniaxial deformation. The molecular structure of the polymer network and its morphological changes during deformation were characterized by using broadband dielectric spectroscopy and in situ synchrotron wide-angle X-ray diffraction, respectively. It was found that the presence of nanoclay introduces a dual crystallization mechanism due to the alignment of nanoparticles during stretching. The improved properties in NR-nanoclay nanocomposites can be attributed to both microstructural and morphological changes induced by nanoclay as well as to the nanoclay mobility in the NR matrix during crystallization. The interplay of these factors during deformation contributes to the formation of a supernetwork structure containing cross-linked chemical chains. nanofiller, and crystallizable networks with similar length scales.