The effect of perspective structure on the computed tomography (CT) value histogram of a three-dimensional (3D) X-ray computed tomographic image was investigated. Images of sphere bead packed beds were taken and the histograms were compared with each other. Normal distributions were fitted to histogram peaks to evaluate histogram shapes. Peaks corresponding to air and alumina were observed in histograms of alumina bead packed beds. The difference between mean values of the peaks decreased and peak standard deviations increased with decreasing bead diameter because of a stronger partial volume effect. Because of this effect, the CT value of a boundary voxel is between CT values of materials present in the voxel. Peaks corresponding to air and glass were observed in histograms of glass bead packed beds. The mean value of the air peak in glass bead packed beds was smaller than that observed in alumina bead packed beds because the specific gravity of glass is smaller than that of alumina. For beds packed with both alumina and glass beads, peak positions of each material differed from those obtained for beds packed with either alumina or glass beads. This indicates that the partial volume effect is caused by boundaries between not only air and beads but also alumina and glass beads. Therefore, the shape of CT value's histogram depends on the 3D structure of the bed. This suggests that the three-dimensional structure can be evaluated on the basis of histogram shape.