Natural rubber (NR) is known as hydrophobic material and is incompatible with hydrophilic filler such as halloysite nanotubes (HNTs). To overcome this obstacle, the compatibilizer is a material of choice to incorporate in such compound. In this study, bio-based compatibilizer was used which was prepared by modification of palm stearin. The presence of special functionalities of modified palm stearin (MPS) was confirmed by Fourier transform infrared (FTIR) analysis. It was then varied from 0.5 phr to 2 phr to the NR matrix. Here, the properties were evaluated through the mechanical properties with special attention to the relationship between their reinforcement and crystallization behavior after stretching. It was found that the addition of MPS significantly enhanced the modulus, tensile strength, and tear strength of the composites. This clearly corresponded to interaction between NR and HNT promoted by MPS. The FTIR spectrum, X-ray diffraction patterns, and scanning electron microscopy images were also utilized to verify the behavior of MPS in the NR/HNT composites. As for the crystallization of the composites, the results obtained from stress–strain curves are in very good agreement to the outputs observed by the synchrotron wide-angle X-ray scattering. This corresponding interaction of MPS has greatly influenced on assisting the strain-induced crystallization of composites.