Display omitted •The structure of CNC suspensions under shear was studied by rheo-SAXS and SALS.•A broad range of lengthscales from nanometer to micrometer has been explored.•Changes in cholesteric organization and disappearance of pitch under shear have been evidenced.•The CNC organization over the three-regime rheological behavior has been clarified.•Buildup mechanisms, from nematic to cholesteric were highlighted on large scales. The breakdown and buildup mechanisms in concentrated cellulose nanocrystal (CNC) suspensions under shear and during relaxation upon cessation of shear were accessed by small-angle X-ray and light scattering combined with rheometry. The dynamic structural changes over nanometer to micrometer lengthscales were related to the well-known three-regime rheological behavior. In the shear-thinning regime I, the large liquid crystalline domains were progressively fragmented into micrometer-sized tactoids, with their cholesteric axis aligned perpendicular to the flow direction. The viscosity plateau of regime II was associated to a further disruption into submicrometer-sized elongated tactoids oriented along the velocity direction. At high shear rate, regime III corresponded to the parallel flow of individual CNCs along the velocity direction. Upon cessation of flow, the relaxation process occurred through a three-step buildup mechanisms: i) a fast reassembling of the individual CNCs into a nematic-like organization established up to micrometer lengthscales, ii) a slower formation of oriented large cholesteric domains, and iii) their isotropic redistribution.