A series of nickel selenides (NiSe2 microcrystals, Ni(1-x)Se and Ni3Se2 microspheres) has been successfully synthesized through a convenient, low-temperature hydrothermal method. A good nucleation and growth environment has been created by forming a uniform and transparent solution reaction system. The compositions (including the x value of Ni(1-x)Se), phase structures, as well as the morphologies of nickel selenides, can be controlled by adjusting the Ni/Se ratio of the raw materials, the pH, the reaction temperatures and times, and so forth. The newly produced Se microspheres in the system have been used as both reactant and in situ template to the Ni(1-x)Se microspheres. It is found that Ni(1-x)Se microspheres act as the intermediate precursor during the formation of Ni3Se2 microspheres. Under certain conditions, hexagonal NiSe microspheres can be converted into rhombohedral NiSe nanowires in solution. The formation mechanisms of a series of nickel selenides has been investigated in detail by means of X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses. This work has provided a general, simple, and effective method to control the composition, phase structure, and morphology of metal selenides in aqueous solution, which will be important for inorganic synthesis methodology and further applications of selenides.