The flow properties of two kinds of cellulose nanocrystal (CNC) rods with different aspect ratios and similar zeta potentials in aqueous suspensions have been investigated. The aqueous CNC suspensions undergo a direct transition from dilute solution to colloidal glass instead of phase separation with the increasing CNC concentration. The viscosity profile shows a single shear-thinning behavior over the whole range of shear rates investigated. The shear-thinning behavior becomes stronger with the increasing CNC concentration. The viscosity is much higher for the unsonicated suspension when compared with the sonicated suspensions. The CNC rods appear arrested without alignment with an increasing shear rate from the small-angle light scattering patterns. The arrested glass state results from electric double layers surrounding the CNC rods, which give rise to long-ranged repulsive interactions. For the first time, we demonstrate that, within a narrow range of CNC concentrations, a shear-induced breakup process of the CNC aggregates exists when the shear rate is over a critical value and that the process is reversible in the sense that the aggregates can be reformed. We discuss the competition between the shear-induced breakup and the concentration-driven aggregation based on the experimental observations. The generated aggregate structure during the breakup process is characterized by a fractal dimension of 2.41. Furthermore, we determine two important variables the breakup rate and the characteristic aggregate size and derive analytical expressions for their evolution during the breakup process. The model predictions are in quantitative agreement with the experimental results.