Abstract Hard carbon (HC) has attracted considerable interest owing to its structural disorder, high sodium storage capacity, and low cost. Although numerous strategies for designing HC structures have been proposed, the origin of structural disorder at the atomic scale remains unclear. In this study, we investigate the relationship between atomic‐level microstructural features and structural disorder in HC. Curved carbon layer models, including the pristine and defective graphene layers, are constructed, among which models contain DV (555–777) defect forms cross‐linking structures under a strain of 90% or less. The structure models are in good agreement with experimental microstructural characterization results of HC in terms of pair distribution function (PDF), XRD, and NMR. It is found that microstructural features in HC, like non‐6‐membered rings and non‐sp 2 hybridized carbon atoms, emerge as interlayer cross‐linking occurs, with their volumetric ratio positively correlating to disordered degree in HC. NMR and electronic structure analyses further indicate that non‐sp2‐hybridized carbon atoms inhibit the graphitization of the structure. Based on the findings, it can be concluded that non‐6‐membered rings and non‐sp 2 hybridized carbon atoms are the primary origin of disorder in HC. This work provides valuable insights for designing HC materials and studying sodium storage mechanisms.