One-shot methods have significantly advanced the field of neural architecture search (NAS) by adopting weight-sharing strategy to reduce search costs. However, the accuracy of performance estimation can be compromised by co-adaptation. Few-shot methods divide the entire supernet into individual sub-supernets by splitting edge by edge to alleviate this issue, yet neglect relationships among edges and result in performance degradation on huge search space. In this paper, we introduce HEP-NAS, a hierarchy-wise partition algorithm designed to further enhance accuracy. To begin with, HEP-NAS treats edges sharing the same end node as a hierarchy, permuting and splitting edges within the same hierarchy to directly search for the optimal operation combination for each intermediate node. This approach aligns more closely with the ultimate goal of NAS. Furthermore, HEP-NAS selects the most promising sub-supernet after each segmentation, progressively narrowing the search space in which the optimal architecture may exist. To improve performance evaluation of sub-supernets, HEP-NAS employs search space mutual distillation, stabilizing the training process and accelerating the convergence of each individual sub-supernet. Within a given budget, HEP-NAS enables the splitting of all edges and gradually searches for architectures with higher accuracy. Experimental results across various datasets and search spaces demonstrate the superiority of HEP-NAS compared to state-of-the-art methods.