<p>The Anqing deposit is a large skarn Cu–Fe deposit within the Anqing–Guichi ore concentration area of the Middle Lower Yangtze River Valley Metallogenic Belt, China. Its zoning pattern is different from the classical pattern with respect to skarn minerals and metals, being characterized by diopside and chalcopyrite at the proximal skarn near the intrusion, while andradite and magnetite occur in the external skarn in contact with marble. In addition, metals (magnetite and chalcopyrite) are more abundant at the middle and upper parts of the intrusion where the dip angle changes from gentle to steep, and gradually pinch out toward the bottom. The formation processes and controlling factors of this geologic phenomenon have not yet been effectively investigated. In this study, we employed numerical modeling based on finite element, coupled with heat transfer, fluid flow, material migration, and chemical reaction, to quantitatively simulate the formation processes of diopside, andradite, magnetite, and chalcopyrite in hydrothermal stages, to reveal the controlling factors of zoning pattern and location mechanism of mineralization in the Anqing deposit. The modeling results indicated that the skarn zonation was governed by the coupled effects of limited wall-rock permeability and chemical species mobility gradients induced by a low-fluorine fluid, while the zoning pattern of metals was mainly controlled by the limited wall-rock permeability. The mineralization reaction lifespan and fluid flux at different positions of the contact zone controlled the spatial distribution of Fe orebody, and the grade and localization of Cu orebody were influenced by the low-permeability characteristics of wall-rock and fluid flux. The contact zone in the mid-upper position of the intrusion, where the dip angle transitions from gentle to steep, was identified as a prospective area for skarn mineralization, providing a potential indicator for future exploration.</p>