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The integration of multiple components with different functionalities into a hierarchical organic nanosystem (HON) has attracted significant attention in optoelectronic applications. However, the rational construction of HONs with ultra-low lattice mismatch (η) remains a major challenge due to the inherent structural incompatibility of different materials. Cocrystal engineering holds great promise as a powerful means to explore the controllable fabrication of HONs, but a systematic demonstration has yet to be achieved. Here, we present a cocrystal engineering strategy for ultra-low lattice mismatch heteroepitaxy of HONs, which exhibits sufficient versatility for integrating a variety of materials to construct HONs. Through experimental synthesis, we have realized a series of representative HONs, including three-segment (η1= 0.7%), branched (η2= 0.8%), and core/shell (η3= 0.6%) nanostructures, with lattice mismatch rates significantly lower than those previously reported for HONs (5%–10%). Furthermore, we selectively synthesized substructures of core/shell, including three-segment and sandwich-like nanowires, revealing the role of interface engineering in the formation of unique HONs. As a conceptual validation, the fabricated HONs have successfully achieved oriented photon signal conversion, laying a solid material foundation for constructing the next generation of integrated optoelectronic devices.