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A series of Late Mesozoic A-type granitoids, including the Xiangshan volcanic-intrusive complex, was recently identified along the Gan-Hang volcanic belt, which was close to the boundary of the Yangtze and Cathaysia blocks in South China. However, significant issues on the petrogenesis of the Xiangshan complex, especially how mantle-derived magma contributes, if any, still remain controversial. In this study, we focused on the apatite geochemistry of the Xiangshan complex to understand the characteristics and evolution of its primary magma. In the Xiangshan complex, mainly including rhyolite, porphyritic lava, granite porphyry, and quartz monzonite porphyry, apatites occur mostly as inclusions in plagioclase and biotite, and exhibit high Srap (Sr content in apatite)/Srhr (Sr content in host rock) (from 0.97 to 3.22, 1.85 on average), indicating these apatites crystalized before plagioclase in the melt. Therefore, the negative Eu anomalies (from 0.06 to 0.83) in apatites of the Xiangshan complex indicate that plagioclase is a remaining stable mineral phase in the source rocks during the partial melting. In addition, most of apatites in the Xiangshan complex with varied whole-rock ASI (aluminum saturation index) values (from 0.88 to 1.19) are characterized by high and relatively homogeneous F content (from 3.14 to 3.55). Therefore, F-rich mineral should be a primary phase in the source. Compared with apatites in three earlier rocks of the complex, apatites from quartz monzonite porphyry have higher Mn and Cl contents, stronger degree of negative Eu anomalies, and lower initial 87Sr/86Sr (0.70642–0.70714), suggesting that before apatites crystalized, the magma to form quartz monzonite porphyry had been mixed with a Cl-rich magma derived from a mantle source that received addition of Cl from subducting oceanic sediments of the Paleo-Pacific plate. The Sr isotope ratios and halogens contents of apatite from quenched dark enclaves found in granitic porphyry imply that the enclaves were formed from this Cl-rich mantle-derived magma through injecting part of this magma into the granitic magma and remaining as quenched enclaves without mechanic mixing and no significant chemical influence on the host granitic magma. Thorough mixing between this mantle-derived magma and the felsic crustal magma did not occur until the latest stage of the Xiangshan volcanism when quartz monzonite porphyry was forming.