Crystal plane nature (including common crystal planes and corresponding roughness) and wettability can provide guidance for more accurate utilization of functional materials. The anisotropic crystal plane nature and wettability of fluorapatite (FAP) crystal were investigated by using macro-photos, scanning electron microscopy (SEM), atomic force microscopy (AFM) and contact angle measurements combined with the density functional theory (DFT). The exposure degree of different surfaces followed the order (001) > (100) > (101) > (111), agreed quite well with the trend in the roughness and the wettability. The DFT calculation based on the density of surface broken bonds explained the cause of the difference of anisotropic crystal plane nature and wettability. That is, differences in the interaction strength between the water molecules and the corresponding surfaces (including hydrogen bonds and O-Ca bonds) were basically small enough to be ignored; however, the number of bonds per unit area was the main influencing factor. The conclusions that were obtained from the experiments were confirmed by a DFT simulation based on the surface broken bonds and atom coordination states. This work demonstrated that the density of surface broken bonds could be an effective and fast indicator to predict the surface properties of materials, and then provided a reference for the application of FAP biomaterial materials.