Cellulose nanocrystals (CNCs) were modified with triazine derivative in an effort to decrease the hydrophilicity of CNCs and improve their thermal stability. In recent decades, much attention has been given to the modification of CNCs to broaden their use in various applications, such as in nanocomposites, as adsorbents for the disposal of wastewater, and so on. The CNCs with a rod-like shape were obtained from cotton through sulfuric acid hydrolysis. Hydrophobic triazine derivative was synthesized via the reaction between triazine and n-butylamine (BA) and then applied to modify CNCs to improve their thermal stability and diminish the hydrophilicity of the nanoparticles. Results of thermogravimetric analysis (TGA) indicated a 150 °C increase in the initial thermal decomposition temperature of modified nanocrystals compared to the original CNCs. The improved thermal stability of modified CNCs was attributed to a shielding effect of the hydrophobic aliphatic amine layer on the surface of the nanoparticles. The results of the dynamic contact angle measurement revealed a decrease of hydrophilicity of the modified CNCs.