The packing characteristics of a pebble bed are essential to understand the heat- and mass-transfer processes occurring within a granular system. Therefore, the packing characteristics of rectangular prismatic pebble beds randomly packed with mono-sized pebbles are analyzed. In terms of the average and local packing fraction distribution, coordination number, and radial distribution function, the effects of the rectangular tube aspect ratio and cross-sectional area on the packing properties of pebble beds are explored in depth. The findings indicate that the packing structures of the rectangular pebble bed exhibit noticeable fixed-wall effects. The average packing fraction and coordination number gradually decline as the rectangular tube aspect ratio rises. Close to the fixed wall, a noticeable wall effect can be seen in the distribution of axial and local packing fractions and the pebble center distribution. The wall effect has an increasing effect on the axial and local packing fraction distributions in rectangular tubes with increasing aspect ratios. Additionally, the average packing fraction and the average coordination number also increase as the cross-sectional area increases, indicating a gradual weakening of the wall effect as the cross-sectional area increases. Furthermore, the cross-sectional area and aspect ratio of the rectangular tubes affect the RDF values of the rectangular pebble beds but have no impact on the RDF features. The findings reported in this paper will be helpful for designing and optimizing pebble beds in the breeding blanket of fusion reactors.