Lithium-ion batteries (LIBs) have been widely applied in portable electronics (laptops, mobile phones, etc.) as one of the most popular energy storage devices. Currently, much effort has been devoted to exploring alternative high-capacity anode materials and thus potentially constructing high-performance LIBs with higher energy/power density. Here, high-capacity anode nanomaterials based on the diverse types of mechanisms, intercalation/deintercalation mechanism, alloying/dealloying reactions, conversion reaction, and Li metal reaction, are reviewed. Moreover, recent studies in atomic-scale storage mechanism by utilizing advanced microscopic techniques, such as in situ high-resolution transmission electron microscopy and other techniques (e.g., spherical aberration-corrected scanning transmission electron microscopy, cryoelectron microscopy, and 3D imaging techniques), are highlighted. With the in-depth understanding on the atomic-scale ion storage/release mechanisms, more guidance is given to researchers for further design and optimization of anode nanomaterials. Finally, some possible challenges and promising future directions for enhancing LIBs' capacity are provided along with the authors personal viewpoints in this research field.