Semi-supervised learning methods have been explored to mitigate the scarcity of pixel-level annotation in medical image segmentation tasks. Consistency learning, serving as a mainstream method in semi-supervised training, suffers from low efficiency and poor stability due to inaccurate supervision and insufficient feature representation. Prototypical learning is one potential and plausible way to handle this problem due to the nature of feature aggregation in prototype calculation. However, the previous works have not fully studied how to enhance the supervision quality and feature representation using prototypical learning under the semi-supervised condition. To address this issue, we propose an implicit-explicit alignment (IEPAlign) framework to foster semi-supervised consistency training. In specific, we develop an implicit prototype alignment method based on dynamic multiple prototypes on-the-fly. And then, we design a multiple prediction voting strategy for reliable unlabeled mask generation and prototype calculation to improve the supervision quality. Afterward, to boost the intra-class consistency and inter-class separability of pixel-wise features in semi-supervised segmentation, we construct a region-aware hierarchical prototype alignment, which transmits information from labeled to unlabeled and from certain regions to uncertain regions. We evaluate IEPAlign on three medical image segmentation tasks. The extensive experimental results demonstrate that the proposed method outperforms other popular semi-supervised segmentation methods and achieves comparable performance with fully-supervised training methods.