The evolution of mesoscale structures of particle packing in binary composite packed beds and their effects on flow characteristics and wall effects were investigated using the discrete element method (DEM) and computational fluid dynamics (CFD). The DEM model was used to build a series of randomly mixed packing structures of particles in accordance with the dynamic change of mass ratio between particles in two size ranges, which were then confirmed by the findings of an X-ray tomography (CT) scan. The results show that the packing structure of b25s75 was conducive to reducing the influence of wall effect in packed bed reactors. For b25s75, the dimensionless distance of radial porosity fluctuation from the wall is 0.3705, which is the smallest among the five packing models, indicating that this structure plays a suppressive role on the wall effect. In addition, the uniformity of velocity and temperature distributions in both the radial and axial directions of different packing structures were compared. The standard deviations of radial relative velocity distributions in the packed beds of b100, b75s25, b25s75 and s100 are 0.28, 0.178, 0.139 and 0.156, respectively, indicating that the stacking mode of b25s75 can make the fluid flow and the gas–solid interactions more uniform.