The infiltration of water droplets in nanochannels is of great importance in microfluidics. In this paper, two types of graphene nanochannels with different wall structures are constructed based on the experimentally reported graphene structure, and the infiltrations of water nanodroplet in the two nanochannels are investigated by performing all-atom molecular dynamics simulation. It is found that the two nanochannels with the same size, composed of different graphene arrays, exhibit completely different infiltration properties: water droplets cannot infiltrate into the multilayer stacked channels, but can wet the vertical array channels spontaneously and completely. By analyzing the structures of the two nanochannels, the novel phenomenon is mainly attributed to the difference in wettability between the inner surface and the outer surface of the nanochannel. From the perspective of energy, the potential energy of water droplets in the multilayer stacked channels is higher than that outside the channels, while the potential energy of water droplets in the vertical array channels is lower than that outside the channels. Therefore, water droplets can spontaneously infiltrate into the latter ones. The van der Waals interaction between the droplet and the channels and the Coulomb interaction inside the droplet play a dominant role in spontaneously infiltrating the water droplets, while the van der Waals interaction inside the droplet has little effect on the infiltration behavior. In addition, through a series of simulations of water droplets wetting the nanochannels with identical inner surface and outer surface, the wettability phase diagram of water droplets infiltration into nanochannels is established, which represents the general law of water droplet infiltration into nanochannels.