Changes of crystal morphology and size of calcium sulfate hemihydrate (HH) by Al3+ ions, synthesized by hydrothermal method, were carried out to understand the interaction mechanism between the metal ion and crystal surface. The preferential adsorption of Al3+ on the top crystal surface was confirmed by XPS and ICP-OES, and the interaction mechanism was evaluated by molecular dynamics (MD). It was observed that the Al3+ ions significantly inhibited the HH growth along c-axial. The shape of HH crystal with the increasing of Al3+ ions concentration (0 to 10 mM), changed from whiskers to short rod-like. The position of Al3+ ions into the structure by molecular dynamics simulation showed preferential adsorption on active sites of (0 0 2) face, which inhibited the growth rate and leaded to the formation of short rod-like HH. This provided a guide for the research of calcium sulfate whiskers preparation from industrial gypsum.