Cellulose nanocrystals (CNCs) have been widely used in reinforcing polymers due to their excellent mechanical properties, whereas the poor compatibility between CNCs and hydrophobic rubber matrices limits their applications in elastomers and flexible devices. Moreover, hydrophobically modified CNCs cannot offer enough increment in mechanical properties because it lowers the interaction related to CNC. We thus introduced thiol-functionalized CNCs (mCNCs) into a nitrile butadiene rubber (NBR) matrix to form covalent linkage between CNC and NBR via thiol-ene click reaction, which was fast, simple, byproduct-little, and controllable. The results from element analysis and Fourier transform infrared spectroscopy showed the thiol substitution degree could be controlled from 0.33% to 0.98%. The obtained nanocomposites showed increased tensile strength (from 0.48 MPa to 2.28 MPa) and elongation at break (from 244% to 526%) as mCNC (0.98%) content increased. The increase in glass-transition temperature (from −30.01 °C to −22.73 °C) proved that the interaction between CNC and NBR was much higher than the interaction between NBR polymer chains. The result also indicated that the increment in mechanical properties was proportional to the thiol substitution degree. This highly efficient method is environmentally friendly and renewable, which can also be used for reinforcing other rubbers.