The Akesayi deposit, located in the eastern part of the Tianshuihai terrane of the Western Kunlun Orogenic Belt, Xinjiang, China, is a recently discovered medium-sized magnetite deposit containing approximately 51 million tons of ore with an average grade of 41 wt%. This deposit is hosted by skarns at the contact between monzonitic granite, diorite porphyry, and medium to low-grade metamorphic clastic rocks of the Permian Huangyangling Group. The ore types include banded, disseminated, and massive ores. The metallogenic process can be divided into prograde skarn, retrograde skarn, oxide, quartz-sulfide, and carbonate stages. The metallic minerals include magnetite and pyrite, and the gangue minerals include olivine, garnet, hedenbergite, hornblende, actinolite, biotite, cummingtonite, chlorite, quartz, and calcite. The zircon U–Pb dating of biotite adamellite intrusion and schist together constrains the formation age of the host rocks in the Akesayi Fe deposit to 217–272 Ma. Rb–Sr dating of eight garnet samples yields an isochron age of 12.41 ± 0.31 Ma, which is almost identical to the 12.56 ± 0.50 Ma age obtained via Sm–Nd dating of eight garnet samples. Furthermore, zircon U–Pb dating yields ages of 12.76 ± 0.12 Ma and 12.37 ± 0.18 Ma for diorite porphyry and monzonitic granite near the Fe orebodies, respectively. The initial Sr isotopes of garnet ((87Sr/87Sr)i = 0.710901) prove that the diorite porphyrite ((87Sr/87Sr)i = 0.709283) is related to skarn mineralization. Thus, the Akesayi deposit is a skarn-type iron ore related to the middle Miocene diorite porphyry. The mineral assemblage indicates the extensive development of manganese-skarn in the Akesayi mining area. The manganese content of host rocks of the deposit is low, and the source of manganese in the skarn may mainly come from the hydrothermal fluids associated with Miocene diorite porphyry emplacement. The compositional variations between the cores and rims of single garnet grains and different stages of tephroite indicate the concentration characteristics of the hydrothermal system, particularly manganese content, which evidently changed during hydrothermal activity. The endmembers of garnet and pyroxene suggest that the ore-forming environment transformed from a relatively reduced acidic environment to an alkali-rich, high-oxygen fugacity environment. The widely developed chlorine-rich amphiboles and biotite indicate that the hydrothermal fluids were rich in chlorine and may have been related to the diorite porphyrite intrusion near the ore bodies. The iron mineralization of the Akesayi deposit is analogous to the Gangdese Miocene porphyry–skarn polymetallic mineralization, which occurred during the Miocene in a post-collisional tectonic setting. Considering the series of Miocene intrusives discovered in West Kunlun, we propose that Miocene skarn Fe mineralization events occurred in West Kunlun, and that this area has great prospecting potential.