Tubercles in sea urchin shells serve as a base on the test plates connecting the spine; these undergo compressive or impact stress from the spines. As the volume fraction of the ordered stereom structure in a tubercle increases, the compressive load–displacement curves are gradually characterized by the typical behavior of ceramic foams. Although this ordered stereom structure only exhibits an average porosity of 50.6%, it also exhibits high fracture resistance and energy dissipation capacity. Such remarkable behavior of the ordered stereom structure is attributed to its unique hierarchical microstructure. Specifically, at the macroscale, the stereom structure is periodic. It has uniformly distributed pores that are typically round, which can effectively reduce the stress concentration around the pores, and the ordered arrangement of the trabeculae along the axial direction of the tubercle bears the most compressive stress. The trabeculae present a bottleneck shape with a specific dimension, ensuring the best fracture resistance with a relatively higher porosity. Furthermore, crack deflection in the trabeculae changes the local fracture mode of the mineral, thereby increasing the crack surface area. Statement of significanceThe connecting bases of the spines in sea urchin shell, known as tubercle, effectively undergo the compressive stress or impact stress from the spines. An ordered stereom structure is found in the tubercle, and it shows an excellent fracture resistance and energy dissipation capacity. Such a fantastic behavior of the ordered stereom structure mainly takes advantage of its unique hierarchical microstructure. The stereom structure presents a periodic structure on macroscale, the trabeculae show a bottleneck shape with a specific dimension to guarantee the best fracture resistance with a relatively higher porosity, and the soft fillers among CaCO3 nanoparticles in a trabecula cause consecutive crack deflections.