In recent decades, catalysis research has transformed from the predominantly empirical field to one where it is possible to control the catalytic properties via characterization and modification of the atomic-scale active centers. Many phenomena in catalysis, such as synergistic effect, however, transcend the atomic scale and also require the knowledge and control of the mesoscale structure of the specimen to harness. In this paper, we use our discovery of atomic-scale epitaxial interfaces in Molybdenum-Vanadium based complex oxide catalysts systems (i.e. Mo-V-M-O, M = Ta, Te, Sb, Nb and etc.) to achieve control of the mesoscale structure of this complex mixture of very different active phases. We can now achieve true epitaxial intergrowth between the catalytically critical M1 and M2 phases in the system that are hypothesized to have synergistic interactions, and demonstrate that the resulting catalyst has improved selectivity in the initial studies. Finally, we highlight the crucial role atomic scale characterization and mesoscale structure control play in uncovering the complex underpinnings of the synergistic effect in catalysis.