Cellulose nanocrystals (CNs) have been proved to be promising reinforcing fillers for rubbers. However, the full utilization of mechanical properties has not been achieved due to random distribution of CNs. In this work, rubber nanocomposites with aligned magnetic CNs were prepared under low magnetic field. Taking tunicate cellulose nanocrystals (t-CNs) as templates, ferroferric oxide (Fe3O4) nanoparticles (NPs) were self-assembled on the surface of t-CNs. The prepared Fe3O4/t-CNs hybrids exhibited high saturated magnetization intensity and can be utilized to align t-CNs in epoxidized natural rubber (ENR) matrix. The anisotropic behaviors of the nanocomposites were characterized and assessed by scanning electron microscopy, transmission electron microscopy, mechanical properties and Halpin-Tsai model, which showed that the hybrids were aligned effectively and the intensity of magnetic field has obvious effect on the anisotropic degree of the hybrids. With 5 phr hybrids, the parallel aligned sample showed 21% and 39% increment in tensile strength and 100% modulus than the perpendicular aligned sample, and 1.4-times and 1.6-times higher than neat ENR. These results indicate the effectiveness of this method to prepare anisotropic rubber nanocomposites.