Two Cu(II)–fluconazole supramolecular isomers 1 and 2 formulated as (flu) 2 Cu(SCN) 2 (flu=fluconazole) have been synthesized and structurally characterized by single crystal X-ray diffraction. Different solvent media lead to the different binding modes of anion SCN − and the flexible C–C chain of fluconazole has been rotated in the two isomers. Complex 1 exhibits a two dimensional square grid-like layer and complex 2 exhibits a two dimensional framework with a parquet motif. Different H-bonds and stacking modes are observed in the two isomers. Complex 1 is nonemissive, whereas complex 2 exhibits photoluminescence property.