Crystalline silicon heterojunction solar cells (SHJ) use intrinsic hydrogenated amorphous silicon (a-Si:H(i)) as a high-performance passivation film for crystalline silicon (c-Si) surface. The high passivation performance is considered to be achieved by hydrogen atoms in the a-Si:H(i) film terminating dangling bonds at the a-Si:H(i)/c-Si heterointerface. It has been reported that the crystallization of the a-Si:H(i) film during the deposition decreases passivation performance. In this study, reactive force-field molecular dynamics (ReaxFF MD) simulations were performed to investigate the effects of the crystallization and the hydrogen concentrations in a-Si:H(i) films on the passivation performance. We prepared a-Si:H(i)/c-Si heterostructure and simulated diffusion of the hydrogen atoms and the crystallization in the a-Si:H(i) films. A simulation system was constructed for the structure of a-Si:H(i) close to the actual structure, and an increase in the crystallinity of the a-Si:H(i) during annealing treatment was obtained. The crystallization was observed to progress with localized hydrogen diffusion close to the a-Si:H(i)/c-Si heterointerface. This suggests that the diffusion of the hydrogen atoms affects the crystallization at a-Si:H(i)/c-Si heterointerface.