In consideration of low cost, simple operation, safe reliability, and environmental benignity, aqueous rechargeable batteries (ARBs) have attracted great interest among portable electronic devices, energy storage, and power source batteries. As the key components of ARBs, the electrode materials lead to a crucial effect for the overall battery properties, such as working voltage, electrocatalytic activity, capacity, and cycling stability. However, owing to the highly reactive aqueous environment, the electrode materials typically demonstrate a series of issues, including active material dissolution, structural instability, and poor catalytic activity, restricting their application. So far, several researchers have devoted much effort to improve the properties of electrode materials for ARBs. In particular, intrinsic structure modification in terms of vacancy regulation, interlayer engineering, and element doping have been applied to optimize the electronic and phase structure of electrode materials, contributing to elevated ion diffusion, fast charge transfer, and adequate active sites for electrochemical reaction. In this review, recent reports are demonstrated about the intrinsic structure modification of electrode materials in aqueous metal‐ion and metal‐air batteries, focusing on various regulation strategies and functional mechanisms. Finally, a brief conclusion and perspective is presented to demonstrate constructive suggestions and opinions for further research.