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The rheological properties and microstructure of nanocrystalline cellulose (NCC) aqueous suspensions have been investigated at different concentrations. The suspension is isotropic up to 3 wt %, and phase separates to liquid crystalline and isotropic domains at higher concentrations where the samples exhibit a fingerprint texture and the viscosity profile shows a three-region behavior, typical of liquid crystals. The suspension behaves as a rheological gel at even higher concentrations where the viscosity profile shows a single shear thinning behavior over the whole range of shear rates investigated. The effects of ultrasound energy and temperature on the rheological properties and structure of these suspensions were studied using polarized optical microscopy and rheometry. Our results indicate that the amount of applied ultrasound energy affects the microstructure of the suspensions and the pitch of the chiral nematic domains. The viscosity profile is changed significantly at low shear rates, whereas the viscosity of biphasic suspensions at intermediate and high shear rates decreased with increasing temperature. This suggests that, between 30 and 40 °C, structural rearrangement takes place. At higher concentrations of about 10 wt %, the temperature has no significant effect on viscosity; however, a marked increase in viscosity has been observed at around 50 °C. Finally, the Cox-Merz rule was found to fail after a critical concentration, thereby implying significant structural formation. This critical concentration is much higher for sonicated compared to unsonicated suspensions.