The computer vision community has witnessed an extensive exploration of vision transformers in the past two years. Drawing inspiration from traditional schemes, numerous works focus on introducing vision-specific inductive biases. However, the implicit modeling of permutation invariance and fully-connected interaction with individual tokens disrupts the regional context and spatial topology, further hindering higher-order modeling. This deviates from the principle of perceptual organization that emphasizes the local groups and overall topology of visual elements. Thus, we introduce the concept of hypergraph for perceptual exploration. Specifically, we propose a topology-aware vision transformer called HyperGraph Transformer (HGFormer). Firstly, we present a Center Sampling K-Nearest Neighbors (CS-KNN) algorithm for semantic guidance during hypergraph construction. Secondly, we present a topology-aware HyperGraph Attention (HGA) mechanism that integrates hypergraph topology as perceptual indications to guide the aggregation of global and unbiased information during hypergraph messaging. Using HGFormer as visual backbone, we develop an effective and unitive representation, achieving distinct and detailed scene depictions. Empirical experiments show that the proposed HGFormer achieves competitive performance compared to the recent SoTA counterparts on various visual benchmarks. Extensive ablation and visualization studies provide comprehensive explanations of our ideas and contributions.