Purpose: The aim of this study was to assess the accuracy of cone-beam computed tomographic (CBCT) images obtained using different voxel sizes in measuring trabecular bone microstructure in comparison to micro-CT. Materials and Methods: Twelve human skull bones containing posterior-mandibular alveolar bone regions were analyzed. CBCT images were obtained at voxel sizes of 0.075 mm (high: HI) and 0.2 mm (standard: Std), while micro-CT imaging used voxel sizes of 0.06 mm (HI) and 0.12 mm (Std). Analyses were performed using CTAn software with the standardized automatic global threshold method. Intraclass correlation coefficients were used to evaluate the consistency and agreement of paired measurements for bone volume (BV), percent bone volume (BV/TV), bone surface (BS), trabecular thickness (TbTh), trabecular separation (TbSp), trabecular number (TbN), trabecular pattern factor (TbPf), and structure model index (SMI). Results: When compared to micro-CT, CBCT images had higher BV, BV/TV, and TbTh values, while micro-CT images had lower BS, TbSp, TbN, TbPf, and SMI values (P<0.05). The BV, BV/BT, TbTh, and TbSp variables were higher with Std voxels, whereas the BS, TbPf, and SMI variables were higher with HI voxels for both imaging methods. For each imaging modality and voxel size evaluated, BV, BS, and TbTh were significantly different (P<0.05). TbN, TbPf, and SMI showed statistically significant differences between imaging methods (P<0.05). The consistency and absolute agreement between micro-CT and CBCT were excellent for all variables. Conclusion This study demonstrated the potential of high-resolution CBCT imaging for quantitative bone morphometry assessment.