Molecule‐based micro/nanocrystal heterojunctions (MMHs) have attracted much attention in the fields of information security, optical sensors, photonic communications, crystal laser media, and miniaturized white‐light device. Although several types of MMHs materials are designed and synthesized, some challenges still need to be recognized and solved, such as in‐depth understanding on the formation–growth mechanisms of low‐dimensional micro/nanostructures and the realization of their practical applications. In this review, recent development of MMHs materials, including basic concepts (i.e., binding force, lattice match, nucleation rate, and crystal interfacial energy), materials classification (from single‐component to multicomponent heterojunctions), preparation methods, together with representative photonic applications, is systematically summarized. This review not only introduces state‐of‐the‐art advances of MMHs systems, but also presents their current issues and future trends, which are favorable to provide new ideas and guidance for expanding the understanding and promoting the evolution of MMHs for advanced optical applications.