The three-dimensional (3D) geological models are the typical and key data source in the 3D mineral prospecitivity modeling. Identifying prospectivity-informative predictor variables from the 3D geological models is a challenging and tedious task. Motivated by the ability of convolutional neural networks (CNNs) to learn the intrinsic features, in this paper, we present a novel method that leverages CNNs to learn 3D mineral prospectivity from the 3D geological models. By exploiting the learning ability of CNNs, the presented method allows for disentangling complex correlation to the mineralization and thus opens a door to circumvent the tedious work for designing the predictor variables. Specifically, to explore the unstructured 3D geological models with the CNNs whose input should be structured, we develop a 2D CNN framework in which the geometry of geological boundary is compiled and reorganized into multi-channel images and fed into the CNN. This ensures an effective and efficient training of CNNs while allowing the prospective model to approximate the ore-forming process. The presented method is applied to a typical structure-controlled hydrothermal deposit, the Dayingezhuang gold deposit, eastern China, in which the presented method was compared with the prospectivity modeling methods using hand-designed predictor variables. The results demonstrate the presented method capacitates a performance boost of the 3D prospectivity modeling and empowers us to decrease work-load and prospecting risk in prediction of deep-seated orebodies.