Two‐dimensional (2D) nanomaterials (i.e., graphene and its derivatives, transition metal oxides and transition metal dichalcogenides) are receiving a lot attention in energy storage application because of their unprecedented properties and great diversities. However, their re‐stacking or aggregation during the electrode fabrication process has greatly hindered their further developments and applications in rechargeable lithium batteries. Recently, rationally designed hierarchical structures based on 2D nanomaterials have emerged as promising candidates in rechargeable lithium battery applications. Numerous synthetic strategies have been developed to obtain hierarchical structures and high‐performance energy storage devices based on these hierarchical structure have been realized. This review summarizes the synthesis and characteristics of three styles of hierarchical architecture, namely three‐dimensional (3D) porous network nanostructures, hollow nanostructures and self‐supported nanoarrays, presents the representative applications of hierarchical structured nanomaterials as functional materials for lithium ion batteries, lithium‐sulfur batteries and lithium‐oxygen batteries, meanwhile sheds light particularly on the relationship between structure engineering and improved electrochemical performance; and provides the existing challenges and the perspectives for this fast emerging field.