Microstructural analysis of porous media has significant research value in the study of their macroscopic properties. An accurate reconstruction of the digital microstructure model is a prerequisite for understanding their physical properties and transport properties. Deep learning can accurately extract features from training images for a fast and precise reconstruction of porous media. The reconstruction methods based on deep learning have yielded important achievements in the reconstruction of porous media. Aiming at the complex morphology and multi-scale image information of porous media, this paper proposes a generic end-to-end deep learning-based encoder–decoder generative method for the reconstruction of porous media from a single 2D image. This paper designs an extended feature pyramid network encoder to extract image features of different resolutions and different scales, and a generator network incorporating multi-scale image information. Through the training process of the network, the final three-dimensional images that meets certain requirements are generated by means of confrontation. By introducing the loss function of the pattern density function and the loss function of Wasserstein distance with gradient penalty, we constrain the reconstructed 3D structures. Finally, the reconstructed 3D structures and the target 3D structures are visualized to compare their similar morphologies. The morphological parameter indicators of the reconstructed 3D structures were line with those of the target 3D structure. The microstructure parameters of the 3D structures were also compared and analyzed. For complex porous media images, our method can achieve diverse, accurate, and stable 3D reconstruction.