Cellulose nanocrystals (CNCs) are bio-based nanoparticles that, under the right conditions, self-align into chiral nematic liquid crystals with a helical pitch. In this work, we exploit the inherent confocal effect of second-harmonic generation (SHG) microscopy to acquire highly resolved three-dimensional (3D) images of the chiral nematic phase of CNCs in a label-free manner. An in-depth analysis revealed a direct link between the observed variations in SHG intensity and the pitch. The highly contrasted 3D images provided unprecedented detail into liquid crystal's native structure. Local alignment, morphology, as well as the presence of defects are readily revealed, and a provisional framework relating the SHG response to the orientational distribution of CNC nanorods within the liquid crystal structure is presented. This paper illustrates the numerous benefits of using SHG microscopy for visualizing CNC chiral nematic systems directly in the suspension-liquid phase and paves the road for using SHG microscopy to characterize other types of aligned CNC structures, in wet and dry states.