A defining feature of a hydrothermal metallogenic system (HMS) is strong structural control on ore mineralization. A systematic analysis of the geometry, kinematics, thermodynamics, and rheology of multiscale ore control structures is crucial for understanding the genesis of HMSs and for ore prospecting. The main challenges include: transitioning from static to multiscale spatiotemporal analysis of the 4D dynamical system involving ore-control structural frameworks, permeability structures, ore-forming fluid pathways, and mineralization deformation networks; identifying key influencing factors of fluid pathways that control ore deposition; and unraveling the mechanism of structure-fluid coupling control of ore formation and localization. This study presents the theoretical and methodological principles and application for developing structural control models for HMSs in the following aspects. (1) The theoretical core. It states that fluid, not structure, is at the core of a structural control model. Fluid flow and ore formation within a hydrothermal system are influenced by the fault zone architecture and permeability structure, where permeability, in linking fluid flow and fluid pressure variation, is key to understanding ore control structures. (2) Stress and pressure dynamics. It considers that differential stress and fluid pressure difference result in diverse combinations of ore control structures, while differences in regional stress field and host rock strength result in variations in mineralization type. (3) Growth of fluid pathways. It considers that fluid pathways initiate from isolated microfractures within the upstream host rocks of overpressured fluid reservoirs which evolve along the direction of the steepest pressure gradient to form new extended fractures through growth and interconnection. These extended fractures eventually interconnect to form fluid pathways. As ore deposition takes place during brief periods of high fluid flux when repeated fault sliding induces rapid changes in fluid pressure, flow velocity, and stress, rapid pressure release—caused by a disruption of dynamic equilibrium in the fluid system due to fluid pathways growth—is a key factor driving metal precipitation. (4) Integrated research. Methodology involves integrating macro and microscopic examination of ore control structures, integrating geological history and stress analysis, combining local and regional analyses, adopting shallow and deep perspectives, and employing a multidisciplinary, multiscale approach to study various ore-controlling factors. (5) Geological mapping. Methodology involves using structure-alteration-mineralization network mapping to characterize alteration-mineralization rock blocks in terms of geometric parameters for ore control structures (such as type, shape, size, occurrence, spacing), and performing quantitative analyses (such as topological analysis of hydrothermal vein-fracture systems, 3D geometric analysis of ore bodies) to determine ore-control structural frameworks and permeability structures and reveal the connectivity of mineralization deformation networks and their ore-forming potential. (6) Numerical modeling. Methodology involves developing geological models, selecting appropriate thermodynamic parameters and dynamic boundary conditions, and utilizing methods such as HCh and COMSOL to perform quantitative simulation of spatiotemporal variations in fluid flow, heat-mass transfer, stress deformation, and chemical reactions during ore formation. This is an effective approach to unveil the mechanism of ore formation controlled by structure-fluid coupling and ore localization pattern, predict ore-forming centers, and identify mineral exploration targets. Based on the above principles, this paper proposes a research methodology for model building, focusing on deriving metallogenic models and ore deposition patterns based on structure-fluid coupling control. Briefly, hydrothermal veins-fracture systems and structure-alteration-mineralization networks are selected as primary research subjects. Research methods include geometric description, kinematic assessment, rheological/dynamic analyses, and thermodynamic synthesis, seeking to delineate ore-control structural frameworks, identify mineralization centers, trace the developments of ore-forming fluid pathways and various mineralization styles, and reveal the spatiotemporal evolution patterns of permeability structures. Additionally, the causal relationship between tectonic reactivation and ore localization is explored. Finally, a metallogenic model based on structure-fluid coupling is constructed to support strategic mineral exploration. This research methodology was applied for mineral prediction in the Jiaojia gold field, Jiaodong Peninsula; its validity and effectiveness were tested and approved.