Organic micro-heterostructures (MHS) with dual optical emissions are essential to produce miniaturized optical waveguides for wavelength division multiplexing technologies. The bimolecular MHS produced by solution-based bottom-up self-assembly technique often leads to poor surface smoothness, edge imperfection, defects, and unwanted thin films deposits. Conversely, sequential sublimation technique at ambient pressure facilitates effective integration of α-perylene micro-square with dicyanomethylene-2-methyl-6-(p-dimethylaminostyryl) 4H-pyran (DCM) microrods in an epitaxial manner to produce MHS. The obtained DCM/perylene MHS act as optical waveguides to produce red (λmax≈670 nm) or/and yellow (λmax≈607 nm) dual optical outputs via an energy transfer mechanism depending upon the heterostructures geometry and optical excitation positions. The presented dual-color emitting MHS optical waveguides are essential for the integrated nano-photonic and optoelectronic device structures. © 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim