Pressure drop is one of the important parameters to study the flow characteristics of packed beds, which contributes to predict the system energy losses and estimate the operating cost. In order to explore the effects of packing forms on pressure drop, a layer-stacking model has been proposed. The model defines two critical parameters—the coverage of layer (k1) and axial packing density (k2) to quantify the radial and axial stacking structures respectively. In this paper, by changing the transverse distance between the centroid of adjacent spheres, a variety of structured packed beds are obtained and its pressure drop are numerically investigated. With the rise of distance, the cross-sectional packing becomes looser and k1 gradually decreases, while axial packing tends to be denser and k2 gradually increases. As a result, the unit pressure drop of the packed bed declines. The flow velocity distribution demonstrates that the decline can be attributed to the reduced velocity in looser packing structures, and the coverage of layer seems to have a greater influence on the pressure drop than the axial packing density. Moreover, an unstable flow is captured in packed beds with enlarged distance. Compared with the mean porosity, the introduction of k1 and k2 provides a more reasonable description of the internal packing state. These findings suggest that the layer-stacking model is helpful for the comprehensive research and optimal design of packed bed reactors.