Cellulose nanocrystals (CNCs) can be used as environmentally friendly additives in drilling fluids. However, their practical performance and utilization principles still need to be further clarified. This paper investigated the effectiveness of carboxylated cellulose nanocrystals (C-CNCs) and sulfonated cellulose nanocrystals (S-CNCs) on the rheological and filtration properties of water-based drilling fluids (WBDFs). The results indicated that at room temperature, 150 celcius, and 180 celcius, both C-CNCs and S-CNCs could be used as rheology modifiers for bentonite WBDFs, and 1.0% of C-CNCs performed the best outstanding viscosity-increasing effect and shear-thinning behavior. Under room temperature and 150 celcius, C-CNCs and S-CNCs with higher concentrations (1.0%) had a better fluid loss reduction effect. However, at 180 celcius, C-CNCs and S-CNCs with lower concentrations (0.5%) showed superior filtration properties, while 1.0% of C-CNCs and S-CNCs unexpectedly increased the fluid loss. Microstructure analysis demonstrated that the addition of CNCs with high concentrations was beneficial for improving the colloidal stability of WBDFs at 150 celcius, while it would produce adverse influence when the temperature was raised to 180 celcius. It was reported that the stiff network among bentonite, CNCs, and immobilized water molecules was destroyed to varying degrees after aging at high temperatures. Especially when a higher concentration of CNCs existed, CNC particles were greatly easier to attract each other, agglomerate, and form many permeation channels, thereby resulting in a decrease of the viscosity and an increase in fluid loss. Therefore, the use of CNCs should be determined according to their characteristics, formation temperature, and other actual operation conditions.