Many studies have been conducted to evaluate the timing of brushing and methods to suppress or halt the progression of acid erosion and initial caries formation, and to restore tooth enamel. However, the analyses in these studies were done from a macroscopic point of view, such as evaluating the change in the hardness of the enamel surface and the change in X-ray permeability, the morphological change due to crystal deposits on the enamel surface has not been elucidated. The purpose of this study was to investigate how crystals on the enamel surface differ when they are in contact with oral cavity liquids such as saliva versus no contact with these liquids. In addition, we assessed the condition of initial caries in which no substantial defect is observable, from the morphological perspective by using elemental analysis and observations with a transmission electron microscope (TEM). We also considered the causes of crystal formation on the enamel surface. As a result, the outermost layer in the pre-eruptive enamel contained a large amount of Mg, which is a stabilizer of amorphous calcium phosphate, suggesting that the layer contains acidic calcium phosphates. It was suggested that tricalcium phosphate, dicalcium phosphate dihydrate, octacalcium phosphate, etc. form a layer on the surface of post-eruptive enamel with no caries and in post-eruptive enamel with caries exposed to saliva in the oral cavity and the layer containing calcium phosphate have higher acid resistance than HAp. The information from this study can be applied to basic clinical research on remineralization therapy and non-invasive treatments of initial caries.