Herein, we report novel supermolecular heterojunctions with six kinds of multi-layer core–shell microstructures, which consist of up to three CT complex components that realize programmable fabrication with defined luminescent CT domains and controllable multi-color-emitting properties. A stepwise seeded-growth route was designed using these CT cocrystals as seed and growing units during the process of fabrication where solution-epitaxy growth would occur based on their perfect lattice matching. This rational multi-step synthetic route furnishes a new insight into developing and constructing more sophisticated organic heterogeneous materials.