Apatite is a ubiquitous mineral in different types of rocks and mineral deposits. Apatite is classified as hydroxyapatite, chloroapatite and fluorapatite according to the species of anions. Apatite is remarkably tolerant to structural distortion and chemical substitution, and thus a series of elements can substitute Ca, P, F, Cl and OH in it, resulting in complex composition of apatite. There are two Ca sites in apatite, the factors controlling the substitution of elements for different Ca sites include ion radius, valence and the types of apatite. Rare earth elements ( REE), Y and Sr are compatible in apatite formed by magmatic process, whereas the compatibility of Cl, F and OH changes with varying physical and chemical conditions. Compared to the extensive study of element partition in melt system, the similar study is rare in hydrothermal system. Apatite Sr, Th, Y, REE contents and Sr/Y ratios can be used to indicate magmatic differentiation and discriminates the types of host rocks. For example, the contents of F, Cl, As and V can distinguish I -type granite from S -type granite, the abundances of REE, Sr, Y, Mn, As and Th, the light rare earth elements (LREE) anomaly and the normalized REE pattern can distinguish the rock types such as carbonate, lherzolite and mafic rocks. The mantle source and its fluid metasomatism can be identified by using the contents of volatile components such as F, Cl and CO, of apatite and its Sr-Nd isotopes. In addition, the variation of Sr/Th and La/Sm in apatite can be used to indicate that the magma originated from dehydrated plates or molten sediments. The content or ratio of major (Mn, F/Cl) and trace elements (Eu) in apatite can be used to indicate the degree of magma fractionation, whereas the ratios of Ce/Pb and Th/U reflect the degree of fluid involvement in magma formation. The contents of variable -valence elements such as Eu, Ce, Ga, and S, and indexes of delta Eu and delta Ce in apatite can be used to infer oxidation-reduction state of magma. Because apatite is very sensitive to hydrothermal metasomatism, the texture and chemical composition of apatite have been widely used in the study of ore-forming processes. In granitite-related critical metal deposits, the contents of major and trace elements and Sr-Nd isotope ratios of apatite are often used to distinguish the source(s) of different granitic magmas, and delta Ce, delta Eu and Mn are used to indicate the oxygen fugacity of granitic intrusions. The contents of F, Cl, S, Mn and F/Cl ratio of porphyry polymetallic deposits can indicate the source and evolution of magma and hydrothermal solution, whereas delta Ce and delta Eu can be used to indicate the oxygen fugacity of magmatic-hydrothermal fluids. The apatite texture, the assemblages of REE minerals, combined with Na, F, Cl and REE contents in iron oxide-copper-gold and iron oxide -apatite deposits can reflect the magma-fluid interaction and the nature of fluids related to mineralization. The differences in the content or ratio of Mn, Fe, REE, Y, F, Cl and SO, can be used to distinguish the mineralization versus barren rocks, and different types of alteration and deposits, which has indicative significance for mineral exploration. Combined with machine learning methods, apatite chemistry can better identify the origin of apatite. In conclusion, apatite, as a new indicator mineral, not only has the ability to constrain petrogenesis and ore genesis, but also has important application prospects in mineral exploration.