The Magushan Cu–Mo deposit is a skarn deposit within the Nanling–Xuancheng mining district of the Middle-Lower Yangtze River Metallogenic Belt (MLYRMB), China. This study presents the results of a new numerical simulation that models the ore-forming processes that generated the Magushan deposit and enables the identification of unexplored areas that have significant exploration potential under areas covered by thick sedimentary sequences that cannot be easily explored using traditional methods. This study outlines the practical value of numerical simulation in determining the processes that operate during mineral deposit formation and how this knowledge can be used to enhance exploration targeting in areas of known mineralization. Our simulation also links multiple subdisciplines such as heat transfer, pressure, fluid flow, chemical reactions, and material migration. Our simulation allows the modeling of the formation and distribution of garnet, a gangue mineral commonly found within skarn deposits (including within the Magushan deposit). The modeled distribution of garnet matches the distribution of known mineralization as well as delineating areas that may well contain high garnet abundances within and around a concealed intrusion, indicating this area should be considered a prospective target during future mineral exploration. Overall, our study indicates that this type of numerical simulation-based approach to prospectivity modeling is both effective and economical and should be considered an additional tool for future mineral exploration to reduce exploration risks when targeting mineralization in areas with thick and unprospective sedimentary cover sequences.