Prompt-based continual learning is an emerging direction in leveraging pre-trained knowledge for downstream continual learning, and has almost reached the performance pinnacle under supervised pre-training. However, our empirical research reveals that the current strategies fall short of their full potential under the more realistic self-supervised pre-training, which is essential for handling vast quantities of unlabeled data in practice. This is largely due to the difficulty of task-specific knowledge being incorporated into instructed representations via prompt parameters and predicted by uninstructed representations at test time. To overcome the exposed sub-optimality, we conduct a theoretical analysis of the continual learning objective in the context of pre-training, and decompose it into hierarchical components: within-task prediction, task-identity inference, and task-adaptive prediction. Following these empirical and theoretical insights, we propose Hierarchical Decomposition (HiDe-)Prompt, an innovative approach that explicitly optimizes the hierarchical components with an ensemble of task-specific prompts and statistics of both uninstructed and instructed representations, further with the coordination of a contrastive regularization strategy. Our extensive experiments demonstrate the superior performance of HiDe-Prompt and its robustness to pre-training paradigms in continual learning (e.g., up to 15.01% and 9.61% lead on Split CIFAR-100 and Split ImageNet-R, respectively).