Cellulose nanocrystals (CNCs) are sustainable nanomaterials commonly employed as biofillers in polymer composites. However, they disperse poorly in hydrophobic polymers in their pristine state, leading to premature failure under stress. Thus, there is an ongoing research effort to enhance the dispersion of CNCs in various polymer matrices to obtain their touted reinforcing potential. In this work, the CNC formation of covalent grafts with epoxidized natural rubber (ENR) and the formation of secondary hydrogen bonds in a base-catalyzed reaction was studied at varying temperatures. The grafting reaction was confirmed using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and toluene swelling experiments. ENR-CNCs processed at 180 °C showed an 83% increase in tensile strength compared to neat ENR. While the 180 °C treated ENR reinforced with CNCs showed superior properties, all temperaturetreated composites exhibited improved tensile strength and elongation at break. Toluene swelling tests confirming the ENR-CNC composites' insolubility treated at 180 and 220 °C. This was corroborated by a 342% increase in Mooney viscosity and improved rheological properties. Overall, the catalyzed thermal treatment of the ENR-CNC composite system generates covalent cross-links between the CNCs and ENR that result in enhanced physicomechanical properties. Such composites could be employed as a masterbatch filler for other hydrophobic rubbers, which can consequently enhance the compatibility of CNCs with the rubbers.