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Organic semiconductor thin films based on polycrystalline small molecules exhibit many attractive properties that have already led to their applications in optoelectronic devices, which can be produced by less expensive and stringent processes. Conduction of electric charges typically occurs in polycrystalline organic thin films. Unavoidably, the crystalline domain size, orientation, domain boundaries and energy level of the interface affect the transport of the charge carriers in organic thin films. In this comprehensive perspective, we focus on highly ordered organic heterojunction thin films fabricated by the weak epitaxy growth method. Transport of charge carriers in these highly ordered organic heterojunction thin films was systematically studied with various characterization techniques. Recent advances are presented in high-performance optoelectronic applications based on highly ordered organic heterojunction thin films, including organic photodetectors, photovoltaic cells, photomemory devices and artificial optoelectronic synapses.