Calcium sulfate hemihydrate whiskers (CSHW), a multi-functional and high value-added building material, were prepared with flue gas desulfurization (FGD) gypsum by hydrothermal method, which could be a reasonable disposal of FGD gypsum. In order to obtain CSHW of a high aspect ratio, a series of manufacturing parameters such as reaction temperature, stirring speed, material–water ratio, and reaction time were investigated. The effect of stabilizing treatment and glycerol concentration on CSHW morphology were also studied by environmental scanning electron microscopy (ESEM) and statistical analysis. The results showed that the optimum preparing conditions of reaction temperature, stirring speed, water–material ratio, and reaction time were 160 °C, 200~300 rpm, 11:1 and 1 h, respectively. Furthermore, stabilizing treatment with octodecyl betaine was necessary for the preparation of CSHW. The final prepared whiskers had smooth surface, uniform morphology, a diameter of 260 nm, and a corresponding aspect ratio of 208.2. Moreover, the addition of glycerol reduced the activity of water, contributing to a lower reaction temperature and much smaller diameter.