NiCoSe₂ microspheres have been successfully synthesized by a facile one-step hydrothermal method at different hydrothermal temperatures. The prepared samples are divided according to their reaction temperatures (90, 120, 150 and 180 °C) and named NiCoSe₂-90, NiCoSe₂-120, NiCoSe₂-150 and NiCoSe₂-180, respectively. The diameters of the NiCoSe₂ microspheres strongly depend on the different hydrothermal temperatures. When the temperature is increased to 150 °C, the size of the resultant NiCoSe₂ microspheres changes from 200 to 800 nm, and the interior of NiCoSe₂-150 possesses a flocculent structure. However, NiCoSe₂-180 displays a cauliflower-like aggregated structure. The prepared NiCoSe₂ alloys are used as high-performance Pt-free counter electrodes (CEs) for dye-sensitized solar cells (DSSCs). Cyclic voltammogram measurement indicates that NiCoSe₂-150 CE has larger current density than Pt CE. Electrochemical impedance spectroscopy shows that NiCoSe₂-150 CE has a low charge-transfer resistance of 1.8 Ω cm². Due to their unique morphologies and well-defined interior and exterior structures, DSSCs based on NiCoSe₂-120 and NiCoSe₂-150 CEs achieve high power conversion efficiencies of 8.48% and 8.76%, respectively, which are higher than that of the solar cell based on Pt CE (8.31%).