Existing open-set learning methods consider only the single-layer labels of objects and strictly assume no overlap between the training and testing sets, leading to contradictory optimization for superposed categories. In this paper, we introduce a more practical Semi-Open Environment setting for open-set 3D object retrieval with hierarchical labels, in which the training and testing set share a partial label space for coarse categories but are completely disjoint from fine categories. We propose the Hypergraph-Based Hierarchical Equilibrium Representation (HERT) framework for this task. Specifically, we propose the Hierarchical Retrace Embedding (HRE) module to overcome the global disequilibrium of unseen categories by fully leveraging the multi-level category information. Besides, tackling the feature overlap and class confusion problem, we perform the Structured Equilibrium Tuning (SET) module to utilize more equilibrial correlations among objects and generalize to unseen categories, by constructing a superposed hypergraph based on the local coherent and global entangled correlations. Furthermore, we generate four semi-open 3DOR datasets with multi-level labels for benchmarking. Results demonstrate that the proposed method can effectively generate and generalize the hierarchical embeddings of 3D objects towards the semi-open environment.