Due to global warming and environmental concerns, developing a fully bio-based nanocomposite is an attractive issue. In this work, the cellulose nanocrystals (CNCs) extracted from Luffa cylindrica, a renewable resource, were explored as a bio-based reinforcing filler in natural rubber (NR) nanocomposites. In addition, modified natural rubber was explored as a potential compatibilizer to assist the filler dispersion in the rubber nanocomposite. The effect of the CNC content (0–15 phr) on cure characteristics and the mechanical, dynamic, and thermal properties of NR/CNC nanocomposites was investigated. The results showed that the scorch time and cure time of the nanocomposites increased with increased CNC contents. The optimum tensile strength of NR nanocomposites having 5 phr of the CNC (NR-CNC5) was 20.60% higher than the corresponding unfilled NR vulcanizate, which was related to the increased crosslink density of the rubber nanocomposite. The incorporation of oxidized-degraded NR (ODNR) as a compatibilizer in the NR-CNC5 nanocomposite exhibited a considerably reduced cure time, which will lead to energy conservation during production. Moreover, the cure rate index of NR-CNC5-ODNR is much higher than using a petroleum-based silane coupling agent (Si69) as a compatibilizer in the NR-CNC5 nanocomposite. The good filler dispersion in the NR-CNC5 nanocomposite compatibilized by ODNR is comparable to the use of Si69, evidenced by scanning electron microscopy. There is, therefore, a good potential for the use of modified NR as a bio-based compatibilizer for rubber nanocomposites.