The rational design and the fine synthesis of organic heterostructures (OHSs) are the key steps toward integrated organic optoelectronics. Herein we have demonstrated a self-assembly approach of combining a molecular-level heterostructure with a structural-level heterostructure and regulating the noncovalent intermolecular interactions for the precise construction of OHSs: a vertical type of anthracene-TCNB heterostructure and a horizontal type of benzopyrene-TCNB heterostructure. The excellent structural compatibility and the low lattice mismatch rate of ∼5.8% between single-component microplates and cocrystal microwires allow anthracene and benzopyrene molecules to grow epitaxially on the cocrystal. Significantly, integrating the multicolor emission and the distinctive dimensional-dependent photon transportation properties of low-dimensional micro/nanostructures, the multicolor optical outputs are achieved via modulating the active/passive optical waveguides in OHSs. Our work exhibits the utilization of the multilevel heterostructure strategy, which boosts the rational design of OHSs for organic photonics.