The Tonglvshan ore field is the most important skarn copper-iron-gold polymetallic ore field in the southeastern Hubei ore concentration area. Since its mineralization is closely related to Tonglvshan stocks, ascertaining the deep distribution and morphologies of these stocks and their contact relationship with surrounding limestones and marbles holds great significance for deep prospecting prediction of the ore field. This study first conducted a detailed analysis of the gravity and magnetic anomaly combinations of the Tonglvshan pluton and stocks; limestones and marbles, as well as their xenoliths; and skarn ore bodies and mineralized bodies. Accordingly, this study inferred the boundary of the Tonglvshan pluton and delineated the xenoliths and mineralized bodies of limestones and marbles within the Tonglvshan pluton. Then, this study conducted the 3D geological modeling based on the results from the 3D physical property inversion and 2.5D and 3D gravity-magnetic human-computer interaction inversion, as well as the drilling and geological data. Finally, this study established a 3D geological model for the plutons and mineralized bodies at depths of 4000 m and below in the Tonglvshan ore field, providing a basis for target delineation and deep prospecting prediction.