In situ studies of strain-induced crystallization in unfilled and multiwalled carbon nanotube (MWCNT)-filled natural rubber (NR) were carried out by using synchrotron wide-angle X-ray diffraction (WAXD). Synchrotron WAXD results indicate that more nuclei appear in the MWCNT-filled NR sample, leading to higher crystallinity, lower onset strain of crystallization, and remarkable enhancement in tensile strength. During deformation, despite the amorphous chains remaining in isotropic orientation, the domains of larger scale (10-100 nm) with high network chain density in the NR matrix are oriented. The MWCNTs induce significant variation of this orientational process, and it is monitored by the stearic acid (SA) crystallites, which are effective nanoprobes of the amorphous phase. The results indicate that a small amount of MWCNTs and SA crystallites can be used as new tools to analyze the microstructural orientation of NR during deformation. The results also yield new insight into the strain-induced crystallization mechanism.