Efficient reference structures are essential in video compression, enabling the exploitation of temporal dependencies across frames to reduce redundancy. In this paper, we delve into the inter-frame reference management mechanism in neural video codecs (NVCs). Previous schemes have inherited the reference propagation mechanism with the guidance of predefined reference structure, but the reference modeling across diverse reference sources remains underexplored. Moreover, the mismatch between the reference structure used for motion estimation and motion compensation limits the effectiveness of inter-frame prediction. To address the above limitations, we propose the unified reference hierarchy that integrates a learned hierarchical reference structure into the existing inherent reference propagation mechanism. Specifically, we first propose the hierarchical reference structure (HRS) to manage the multiple temporal contexts in the propagated reference feature, where a hierarchy-aware reference modulation module is integrated to select the most relevant reference features across different quality levels under the guidance of the reference balance loss. In addition, we propose the HRS-guided feature-wise inter-frame prediction that learns the low-rank approximation of the selected reference feature for ensuring the consistency and improving the inter-frame prediction performance. We conduct experiments on a state-of-the-art NVC, DCVC-DC. Experimental results show that our codec achieves an average 26\% bitrate saving over H.266/VVC, and a 28.2\% bitrate reduction compared to DCVC-DC without increasing the decoding complexity.