The Lintan gold deposit, located in the “gold triangle” of Qianxinan, Guizhou Province, has become a focal point for implementing the “exploring near existing deposits” strategy, aiming to identify another large-scale gold deposit within the region. This study addresses the challenges of deep-edge mineral exploration in the Lintan gold deposit by adopting a metallogenic system perspective. Using a multidisciplinary approach, it integrates geological, geophysical, and geochemical datasets to construct various three-dimensional (3D) visualization and prospectivity models. The research leverages geostatistical theories and methods, multisource digital information analysis, and advanced 3D modeling and visualization techniques to verify mineralization anomalies. These efforts expand the scope of prospectivity evaluation for the deep-edge regions of the Lintan gold deposit into 3D space. In the 3D spatial framework, this study elucidates the metallogenic geological characteristics, geophysical anomalies, and geochemical signatures within the study area. Building upon this foundation, it conducts a comprehensive analysis and evaluation of geological, geochemical, and geophysical prospecting indicators under multisource geoscience datasets. This approach transitions from known to unknown domains, effectively reducing the ambiguities and uncertainties associated with single-source data interpretations. The findings demonstrate that, under the guidance of geological prospectivity models, the effective integration and synthesis of geological, geophysical, and geochemical data can reveal the interrelationships between metallogenic geological bodies and the contributing factors of the metallogenic system. This enables the identification of anomalous information associated with metallogenic geological bodies and facilitates the spatial localization and prediction of target areas for deep-edge mineral resources. The proposed methodology provides novel insights and techniques for deep-edge mineral exploration. Comprehensive analysis indicates significant prospectivity for mineral resource exploration in the deep-edge regions of the Lintan gold deposit.