Rational design of elaborate, multicomponent nanomaterials is important for development of many technologies such as optoelectronic devices, photocatalysts, and ion batteries. Combination of metal chalcogenides with different anions, like in CdS/CdSe structures, is particularly effective for creating heterojunctions with valence band offsets. Seeded growth, often coupled with cation exchange, is commonly used to create various core/shell, dot-in-rod, or multi-pod geometries. To augment this library of multi-chalcogenide structures with new geometries, we have developed a method for post-synthetic transformation of copper sulfide nanorods into several different classes of nanoheterostructures containing both copper sulfide and copper selenide. Two distinct temperature-dependent pathways allow us to select from several outcomes—rectangular, faceted Cu<sub>2-x</sub>S/Cu<sub>2-x</sub>Se core/shell structures, nanorhombuses with a Cu<sub>2-x</sub>S core and triangular deposits of Cu<sub>2-x</sub>Se, or Cu<sub>2-x</sub>(S,Se) solid-solutions. These different outcomes arise due to the evolution of molecular components in solution. At lower temperatures, slow Cu<sub>2-x</sub>S dissolution leads to concerted morphology change and Cu<sub>2-x</sub>Se deposition, while Se-anion exchange dominates at higher temperatures. We present detailed characterization of these Cu<sub>2-x</sub>S-Cu<sub>2-x</sub>Se nanoheterostructures by TEM, PXRD, EDS, and STEM-EDS. Furthermore, we correlate the selenium species present in solution with the roles they play in the temperature-dependence of nanoheterostructure formation by comparing the outcomes of the established reaction conditions to use of didecyl diselenide as transformation precursor.