The cell orientation characteristics of the natural combs of honey bees have received much research attention. Although natural combs have been shown to be composed of cells with three orientations—vertical, intermediate (oblique), and horizontal—the proportion of comb cells in these three orientations varies. Knowledge of the comb-building preferences of honey bees is essential for the installation of wax comb foundations, and clarification of the cell orientation characteristics of natural honey bee combs is important for beekeeping. The purpose of this study was to determine the cell orientation characteristics of natural combs of Eastern honey bees (Apis cerana cerana) and Western honey bees (Apis mellifera ligustica). Newly built combs were used to measure the orientation of hexagonal cells and calculate the proportion of cells in different orientations relative to the total number of cells. The number of eggs laid by queens in the cells of different orientations was also determined. The orientation of cells in the natural combs of Eastern and Western honey bees was determined based on the value of the minimum included angle between the pair of parallel cell walls and a vertical line connecting the top and bottom bars of the movable frame in the geometric plane of the comb: 0°≤θ≤10°, 10°<θ≤20°, and 20°<θ≤30° for vertical, intermediate, and horizontal orientations, respectively. Natural combs were composed of cells with at least one orientation (vertical or horizontal), two orientations (vertical + intermediate (oblique) or vertical + horizontal), or three orientations (vertical + intermediate + horizontal), and the proportions of combs with the three aforementioned configurations differed. Both Eastern honey bees and Western honey bees preferred building combs with cells in a vertical orientation. Queens showed no clear preference for laying eggs in cells of specific orientations. The results of this study provide new insight that could aid the production and cutting of wax comb foundations of Eastern and Western honey bees. Our study highlights the importance of installing wax comb foundations compatible with the comb-building preferences of bees.