Herein, we present a comprehensive investigation of rationally designed zinc selenide (ZnSe) nanostructures to achieve highly negatively charged ZnSe nanostructures. A Microwave-assisted hydrothermal synthesis method was used to synthesize three types of ZnSe nanostructures, i.e., nanorods, µ-spheres and nanoclusters, as characterized by a zeta potential analyzer, X-ray diffraction (XRD), scanning electron microscopy (SEM), Raman spectroscopy and BET, which were labeled as type A, B and C. Three different solvents were used for the synthesis of type A, B and C ZnSe nanostructures, keeping other synthesis conditions such as temperature, pressure and precursors ratio constant. Based on two heating time intervals, 6 and 9 h, types A, B and C were further divided into types A6, A9, B6, B9, C6 and C9. ZnSe nanostructures were further evaluated based on their fluorescent quenching efficiency. The maximum fluorescence quenching effect was exhibited by the ZnSe-B6 type, which can be attributed to its highly negative surface charge that favored its strong interaction with cationic dye Rhodamine B (Rh-B). Further, the optimized ZnSe-B6 was used to fabricate an aptasensor for the detection of a food-based toxin, ochratoxin-A (OTA). The developed aptasensor exhibited a limit of detection of 0.07 ng/L with a wide linear range of 0.1 to 200 ng/L.