A significant proportion of recent mineral exploration has increasingly focused on the targeting of deep-seated orebodies. Mineral prospectivity modeling is one of the more important approaches that facilitates exploration targeting and the mitigation of risks associated with mineral exploration, particularly under cover. Recent advances in 3D mineral prospectivity modeling enable the effective extraction of predictive information from three-dimensional geological models, enabling more accurate exploration targeting of deep-seated orebodies. These advancements have synergized with deep learning approaches to improve the efficiency of mineral exploration based on nonlinear and multi-layer sensing attributes, effectively enabling the identification and extraction of key relationships between 3D predictive maps and mineralization. The main deep learning method used for 3D mineral prospectivity modeling is convolutional neural network (CNN) modeling. However, this research typically does not consider the multiscale features of geological structures, meaning further improvements can be made to this modeling approach. This paper introduces a multi-scale 3D convolutional neural network model (3D CNN) incorporating a spatial attention mechanism and an Inception module (MSAM-CNN) for 3D mineral prospectivity modeling. By integrating Inception modules and spatial attention mechanisms, the network's capability to identify multi-scale geological features and delineate key predictive areas is significantly enhanced compared to typical CNN approaches. This new approach provides further improvement in the accuracy and generalization capability of 3D mineral prospectivity modeling. To evaluate the effectiveness of this model, we undertook 3D mineral prospectivity modeling within the area of the Baixiangshan iron deposit, in the Ningwu Basin of the Middle-Lower Yangtze River Metallogenic Belt, China. The results show that the multi-scale 3D convolutional neural network model is remarkably robust and has good generalization capabilities. The approach can also can effectively delineate targets within the deep and peripheral areas of the deposit, providing targets for future exploration. The addition, performance indicators, ROC curve, and Capture-Efficiency curve generated during this modeling consistently demonstrate that the MSAM-CNN model outperforms Inception-enhanced CNN (M-CNN), CNN, Random Forest (RF), and Support Vector Machine (SVM) models. All of this indicates that MSAM-CNN approaches can effectively extract 3D spatial features within 3D predictive maps during 3D mineral prospectivity modeling better than other approaches that are commonly used, indicating that thius approach represents a promising tool for the accurate and precise identification of targets during future exploration for deep-seated mineralization.