The purpose of this study was to analyze the effectiveness of newly developed dental dual-energy (DE) cone-beam computed tomography (CBCT) to compare both the voxel values in hard bone tissue of DE-CBCT and multidetector computed tomography (MDCT) images, collected in a clinical trial conducted at Seoul National University Dental Hospital. A software implemented as a scripted module of a three-dimensional (3D) slicer was developed to register the volume data from the MDCT space to DE-CBCT, locate the same 3D regions of interest (ROIs) in each image space, and extract the statistics of the ROIs. The mean values were paired and used as representative values of the ROIs. A scatter plot with the line of equality and Bland–Altman (BA) plot of difference for a pair of measured means were used for statistical analysis. Of the ROI pairs, 96% were within ±15% from the identity line, and more than 95% of the measured ROI pairs were within the limits of agreement of the 95% confidence intervals (CIs), with the CI of the limits in BA plots. The newly developed dental DE-CBCT showed a level of voxel value accuracy similar to that of MDCT.