Reliable segmentation of pores and minerals from high-resolution (HR) digital rock data is the fundamental prerequisite for accurately characterizing the digital rock's physical properties. Limited by the complexity of the super-resolution (SR) issues and the user bias for segmentation, conventional SR enhancement and segmentation methods are generally brutal in satisfying the research demands. In recent years, with the introduction of deep learning technology into digital rock research, deep learning-based approaches for SR enhancement or segmentation methods have emerged and achieved significantly better effects than conventional approaches. Most deep learning-based digital rock SR enhancement and segmentation processing steps are currently separate. Still, preliminary studies have demonstrated that an end-to-end approach that integrates the two steps could achieve better performance. However, the training cost of 3D deep neural networks that can be directly applied to 3D digital rock processing is usually expensive. In contrast, 2D networks cannot be effectively applied to SR segmentation of 3D digital rocks. Here, we present an end-to-end SR segmentation framework for 3D digital rock based on a 2D multi-task joint deep neural network. The multi-task joint networks utilize a parallel architecture that integrates the SegNet for the segmentation task and the EDSR for the SR task. We also improved the loss function to address the issue of category imbalance and proposed an approach to utilize the 2D network for 3D digital rock processing. We demonstrate the effectiveness of the proposed network framework, the improved loss function, and the 3D digital rock processing strategies through ablation experiments on the high and low-resolution (LR) CT image datasets captured by imaging devices. The results show that the evaluation metrics and physical properties of the SR-segmented 2D\\3D digital rocks align with the HR-segmented results (ground truth). It indicates that the proposed framework can improve the performance of digital rock SR enhancement and segmentation and that it is essential to integrate deep learning frameworks into digital rock analysis.