Calculating the spatial structures of ion crystals is important in ion-trapped quantum computation. Here we demonstrate that the simulated annealing method is a powerful tool to evaluate the structures of ion crystals. By calculating equilibrium positions of 10 ions under harmonic potential and those of 120 ions under anharmonic potential, both with the standard procedure and simulated annealing method, we find that the standard procedure to evaluate spatial structures is complicated and may be inefficient in some cases, and that the simulated annealing method is more favorable. Calculating the spatial structures of ion crystals is important in ion-trapped quantum computation. Here we demonstrate that the simulated annealing method is a powerful tool to evaluate the structures of ion crystals. By calculating equilibrium positions of 10 ions under harmonic potential and those of 120 ions under anharmonic potential, both with the standard procedure and simulated annealing method, we find that the standard procedure to evaluate spatial structures is complicated and may be inefficient in some cases, and that the simulated annealing method is more favorable.