The impact of the particle size and wettability on the orientation and order of assemblies obtained by self-organization of functionalized microscale polystyrene cubes at the water/air interface is reported. An increase in the hydrophobicity of 10- and 5-μm-sized self-assembled monolayer-functionalized polystyrene cubes, as assessed by independent water contact angle measurements, led to a change of the preferred orientation of the assembled cubes at the water/air interface from face-up to edge-up and further to vertex-up, irrespective of microcube size. This tendency is consistent with our previous studies with 30-μm-sized cubes. However, the transitions among these orientations and the capillary force-induced structures, which change from flat plate to tilted linear and further to close-packed hexagonal arrangements, were observed to shift to larger contact angles for smaller cube size. Likewise, the order of the formed aggregates decreased significantly with decreasing cube size, which is tentatively attributed to the small ratio of inertial force to capillary force for smaller cubes in disordered aggregates, which results in more difficulties to reorient in the stirring process. Experiments with small fractions of larger cubes added to the water/air interface increased the order of smaller homo-aggregates to values similar to neat 30 μm cube assemblies. Hence, collisions of larger cubes or aggregates are shown to play a decisive role in breaking metastable structures to approach a global energy minimum assembly.