The simulation system that yields reliable physicochemical properties of ammonium perchlorate (AP) such as lattice energy, solution density, diffusion coefficient, and radial distribution functions was constructed. Dissolution of AP in water was computationally confirmed to be an endothermic reaction, which corresponds to the fact that crystallization of AP from an aqueous solution is an enthalpically favored process. On the basis of the YasuokaMatsumoto method, the MD simulation on the homogeneous nucleation of AP from an aqueous solution was carried out, and the calculated nucleation rate was shown to be 1 order of magnitude different from that predicted by the classical nucleation theory (CNT). The critical sizes of nucleus (12 and 8 at S = 5.1 and 6.4, respectively) are also very close to those estimated by the CNT (12.4 and 8.2 at S = 5.1 and 6.4, respectively). The free energy of nucleation obtained from the cluster size distribution definitely shows the energy barrier for nucleation, which is consistent with the trends predicted by the CNT. The time-dependent concentration and maximum cluster size obtained by the present simulation clearly show that the crystallization of AP can be divided into two stages, nucleation and nuclei growth. At the earlier stage a lot of nuclei are spontaneously formed, and at the stage of nuclei growth AP molecules tend to be incorporated into the existing nuclei and continuously merged into a larger one.