A method is proposed for the prospecting prediction of subsurface mineral deposits based on soil geochemistry data and a deep convolutional neural network model. This method uses three techniques (window offset, scaling, and rotation) to enhance the number of training data for the model. A window area is used to extract the spatial distribution characteristics of soil geochemistry and measure their correspondence with the occurrence of known subsurface deposits. Prospecting prediction is achieved by matching the characteristics of the window area of an unknown area with the relationships established in the known area. This method can efficiently predict ore prospective areas where there are few ore deposits used for generating the training dataset, meaning that the deep-learning method can be effectively used for deposit prospecting prediction. Using soil active geochemical measurement data, this method was applied in the Daqiao area, Gansu, for which seven favorable gold prospecting target areas were predicted. The new method should be applicable to prospecting prediction using conventional geochemical data in other areas.