Understanding the defect structure is fundamental to correlating the structure and properties of materials. However, little is known about the defects of soft matter at the nanoscale beyond their external morphology. We report here on the molecular-level structural details of kink defects of cellulose nanocrystals (CNCs) based on a combination of experimental and theoretical methods. Low-dose scanning nanobeam electron diffraction analysis allowed for correlation of the local crystallographic information and nanoscale morphology and revealed that the structural anisotropy governed the kink formation of CNCs. We identified two bending modes along different crystallographic directions with distinct disordered structures at kink points. The drying strongly affected the external morphology of the kinks, resulting in underestimating the kink population in the standard dry observation conditions. These detailed defect analyses improve our understanding of the structural heterogeneity of nanocelluloses and contribute to the future exploitation of soft matter defects.