Integration of two-dimensional (2D) nanomaterials and their composites into energy storage devices, especially rechargeable batteries, offers opportunities to timely tackle the challenges of ever growing clean and sustainable energy demands. Therefore, it is crucial to design hybrid 2D electrode materials for high performance rechargeable batteries and to fundamentally understand their storage mechanisms at the atomic or nanoscopic levels. This review firstly describes some of the exciting progress achieved in the economic production of graphenes, 2D transition metal dichalcogenides (TMDCs), and their composites. Then we survey the recent developments in their electrochemical energy storage pathways and present the associated three kinds of storage mechanisms. In addition, we highlight the uncovered structure-performance relationships while utilizing advanced microscopic techniques, such as in situ high resolution transmission electron microscopy (TEM) and spherical aberration-corrected scanning TEM (STEM), both leading to deep unveiling and understanding of the atomic-scale ion storage/release mechanisms and hence providing clear guidance for designing optimized 2D nanostructured electrode materials. Finally, the major challenges and opportunities that researchers have to face in this field are outlined. We hope that this review can deepen the Chemical and Material Science Communities' understanding of this field and thus effectively contribute to the smart design of future-generation 2D nanostructured electrodes and exploitation of their microscopic mechanisms toward novel high-performance rechargeable batteries.