The difference of mineral properties is the basic condition of flotation. Studying the difference of crystal structure characteristics between fluorapatite and dolomite is helpful to understand its flotation behavior and micro-mechanism. To understand the differences in crystal and surface properties of fluorapatite and dolomite, the first-principles method based on density functional theory was used to study the crystal structure and surface properties of fluorapatite and dolomite from a microscopic perspective, and the adsorption mechanism of oleic acid ions on the surface of fluorapatite and dolomite was revealed. The results show that the activity of metal atoms in fluorapatite and dolomite crystals is different. The activity of Ca atoms in dolomite crystals is greater than that of Mg atoms. The reactivity of Ca atoms in fluorapatite crystals is low, and the reactivity of F and O atoms is high. After the surface of fluorapatite is formed, the surface of fluorapatite is mainly dominated by the fracture of F–Ca bond and O–Ca bond. The surface of dolomite is mainly dominated by the fracture of O–Ca bond and O–Mg bond. The ionicity of O–Ca bond in fluorapatite crystal is stronger, and the activity of Ca site on the surface of fluorapatite is greater than that on the surface of dolomite. The reactivity of Ca atoms on the surface of dolomite (104) is stronger than that of Mg atoms. NaOL undergoes chemical reactions on the surface of fluorapatite (001) and dolomite (104). The chemical effect of oleic acid ions on the Ca site of dolomite (104) surface is stronger than that on the Mg site. The effect of water molecules on the adsorption strength ratio of oleic acid ions on dolomite surface is less than that of water molecules on the adsorption strength of oleic acid ions on fluorapatite surface. In the absence of other conditions, the interaction strength of fluorapatite and dolomite with water molecules is similar, and the interaction between water molecules and dolomite is slightly larger than that between fluorapatite and water molecules. The effect of oleic acid ion dolomite is stronger than that of fluorapatite; the interaction between HEDP and fluorapatite is stronger than that between HEDP and dolomite.