Unsaturated polyester resin (UPR) has been modified with a liquid epoxidized natural rubber (LENR). The addition of LENR improves the toughness, but it is inevitably accompanied by a significant loss in stiffness, yield strength, and thermal resistance. Incorporation of a rigid material into the LENR–UPR blend, such as cellulose nanocrystal (CNC), provided a ternary polyester nanocomposites with desire mechanical properties. In the present work, the effects of different CNC and LENR content on the nanocomposite morphology and mechanical properties were examined. Morphological studies revealed that the size of the rubber particles is independent of the rubber content due to the chemical interaction of rubber and matrix; however, the size of the LENR particles increased with increasing CNC content. Tensile tests indicated that the blend’s tensile strength and elastic modulus could be further improved by incorporation of the CNCs. The high crystallinity and surface area of CNCs were the main factors for improvement of tensile properties of the blend. Moreover, the impact energy of the UPR improved when it was modified with the LENR, and even further improvement was achieved with the CNC addition to form nanocomposites. Dynamic mechanical thermal analysis (DMTA) showed that the storage modulus of nanocomposites with 1.5wt% rubber content was lower than those with 4.5wt% LENR; however, both samples showed a higher storage modulus than the neat UPR and the unfilled blend. The glass transition temperature (Tg) of the UPR decreased with the LENR addition, but improved with the addition of CNCs. The nanocomposites prepared with a higher LENR content displayed better mechanical properties than those with low LENR content.