The ligament of bivalve molluscs is known for its exceptional mechanical properties. In the present work, we investigated the nanoscale structure and composition of the aragonite fibers in the inner ligament of the freshwater shell Hyriopsis Cumingii, using high-resolution transmission electron microscope coupled with selected area electron diffraction, field-emission scanning electron microscope, and X-ray diffraction. The sample was found to exhibit cobble-like nanograins that were the basic building blocks to construct individual needle-shaped aragonite fibers in the ligament, which are generally different in sizes and shapes. The individual aragonite fibers were confirmed to be polycrystalline. In addition, twin stacking faults have been observed in the aragonite fibers of the ligament. These newly identified structural properties enhance our understanding of the formation mechanisms of bivalve ligaments and provide new guidelines to design and synthesis advanced functional materials for biomedical applications.