Using microscopy imaging techniques, X-ray scattering, and nonlinear rheological measurements, we have examined microstructural changes, and phase behavior of cellulose nanocrystals (CNC)/montmorillonite (MMT) composite colloidal systems. Fourier-transform (FT) rheology-stress decomposition methods, Lissajous-Bowditch plots, and other techniques are used to both qualitatively and quantitatively determine the various phases that the suspensions exhibit. In the MAOS (medium amplitude oscillatory shear) region, multiple scaling regions, as well as quadratic scaling regions are obtained. The dependence of the normalized third relative intensity (I 3/1) values on angular frequency (ω) also provided new insights into how nonlinear parameters depend on the various CNC/MMT phases. These findings allow us to differentiate various phases exhibited by the composite system, including the isotropic, biphasic, and chiral nematic liquid crystalline (LC) phases. The CNC/MMT nanocomposite system exhibits a variety of liquid crystalline phases, which may contribute to improved mechanical properties for the system, including increased mixture strength, stiffness, and toughness because of the particle alignment in the LC phase. Additionally, the field of optics and photonics may find use for this nanocomposite system in the fabrication of sensors, polarizers, and optical films; energy storage applications where the aligned structures facilitate ion transport; and the formulation of paints and coatings where the strain stiffening and shear thinning behavior of the CNC/MMT composite system are critical.