Introducing defects is an effective approach to promote the lithium ion storage ability of host material. Constructing pure defects is beneficial to understand the lithium ion storage mechanism in the defects. Herein, we fabricate defective graphene without intricate functional groups via a flash Joule heating (FJH) technique within a mere 1 ms. The FJH-reduced graphene lattice harbors a multitude of defects, and its unique three-dimensional structural network enables an ultra-high lithium ion storage capacity. Moreover, the highest capacity of F-RGO-5 reaches 2500 mAh/g in the 800th cycle, its three-dimensional architecture allows it to withstand high currents and prolonged cycles without drastic failures. Nascent defects and defect-induced lithium plating predominantly contribute to capacity enhancement during cycling, while dendrite formation primarily leads to decay. Our findings present an approach to defect-based designs of high-capacity lithium anodes and provide valuable insights into their energy storage mechanisms.