Our universe is hierarchical. In the bottom-up scenario, smaller structures form larger systems by merging. The hierarchy clustering algorithm can visualize such structures in a clear way. It organizes objects into a hierarchical tree by calculating their pairwise binding energy. This method can effectively identify structures at various levels from substructures to groups and clusters, even to superclusters, without depending on prior assumptions such as hydrostatic equilibrium or morphological symmetry. We apply it to galaxy clusters, substructures, and even star clusters, it provides a new approach to study gravity-linked systems in the hierarchical universe.