Cellulose nanocrystals (CNCs) have great application potential as environmentally friendly and multifunctional additives in drilling fluids. But their practical performance and utilization principles still need to further clarify. This paper investigated the effectiveness of two kinds of typical CNCs, including carboxylated cellulose nanocrystals (C-CNC) and sulfonated cellulose nanocrystals (S-CNC), on the rheological and filtration properties of water-based drilling fluids (WBDFs) under different concentrations. The results indicated that at room temperature, 150℃, and 180℃, both of C-CNC and S-CNC could be used as rheology modifiers for bentonite WBDFs, and 1.0% of C-CNC performed the best outstanding viscosity-increasing effect and shearthinning behavior. The fitting results of rheological models showed that all of the samples are closest to the Hersche-Bulkley model. Under room temperature and 150℃, C-CNC and S-CNC with higher concentrations (1.0%) had a better fluid loss reduction effect. However, at 180℃, C-CNC and S-CNC with lower concentration (0.5%) showed superior filtration property, while 1.0% of C-CNC and S-CNC unexpectedly increased the fluid loss. In the whole, C-CNC performed better properties in rheological modification and fluid loss reduction than S-CNC. Microstructure analysis demonstrated the dispersion stability of C-CNC was better, and these nanoparticles easily adsorbed onto bentonite and exhibited strong gel formation capacity. The addition of CNCs with high concentrations was beneficial for decreasing the zeta potential of WBDFs and improving their colloidal stability at 150℃, while it would produce adverse influence when the temperature was raised to 180℃. It was referred 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 CNC existed, CNCs particles were greatly easier to attract each other, agglomerate, and form many permeation channel, thereby resulting in decrease of the viscosity and increase of the fluid loss. Therefore, it was suggested that the use of CNCs should be determined according to their characteristics, formation temperature, and other actual operation conditions.