The Gejiu polymetallic tin ore cluster developed a series of basic-intermediate-acidic-alkaline magmatic rocks during the Late Yanshan period, the genesis and evolution of which are crucial for an in-depth understanding of the Gejiu tin-copper symbiosis and the formation processes of various types of tin ores. However, the nature of the granite source area, the type of genesis, and the evolutionary processes related to the ore-forming process remain widely debated. As a pervasive mineral, the trace element characteristics of apatite can serve as a tracer for magma-fluid evolution process and fluid alteration process. Therefore, this study focuses on apatite in different types of rocks from Gejiu as the research object, and through EPMA and LA-ICP-MS analysis, the main and trace element content characteristics of apatite in each rock body were obtained. Using the fractionation characteristics of rare earth elements, combined with various trace elements with typical discrimination, the granite of different source areas and different types of genesis were indicated. The results show that the Shenxianshui K-feldspar granite and Longchahe monzogranite developed in the western part of the Gejiu fault are crust-mantle mixed-source I-type granites, and their apatite is of magmatic type, with a right-skewed distribution trend of rare earth elements, and high Sr (135×10^-6~280×10^-6), V (0.86×10^-6~28.6×10^-6), Ce (2 147×10^-6~6 541×10^-6), high Th/U (2.09~6.93), and La/Sm (2.27~5.45) characteristics. This type of granite body has not formed tin, copper, and other metal ore deposits. The Laoka biotite granite, muscovite granite, and sericite granite distributed in the eastern part of the Gejiu fault are S-type granites derived from meta-sedimentary rocks and are the main carriers of tin, copper, and tungsten ore formation. Their apatite is mainly of hydrothermal type, with a relatively flat rare earth element pattern, and has higher Mn (337×10^-6~4 415×10^-6) content and lower V (0.14×10^-6~11.6×10^-6), La (190×10^-6~1 440×10^-6), Ce (706×10^-6~4 856×10^-6) content, as well as lower La/Sm (0.52~3.03). These characteristics reveal the rock-forming and ore-forming specificity of apatite in the Late Yanshan magmatic rocks of Gejiu, and indicate that different source magma coexisted on both sides of the Gejiu fault during the same period, providing new insights into the rock-forming and ore-forming processes of the Gejiu ore cluster.