Covalent organic frameworks (COFs) are a class of porous crystalline materials with high surface areas, tunable pore sizes, and customizable surface chemistry, making them ideal for selective metal ion separation. This review explores the nanoarchitectonics, mechanisms, and applications of COFs in metal ion separation. We highlight the diverse bonding types (e.g., imine, boronic ester) and topologies (2D and 3D) that enable precise separation for alkali, alkaline earth, transition, and precious metals. The influence of COFs' pore characteristics, such as surface area, pore size, and distribution, on their adsorption capacity and selectivity is discussed. Additionally, surface functionalization enhances ion adsorption through electrostatic, coordination, and polarity interactions. Despite significant progress, challenges remain, including optimizing functional design for complex metal systems, improving material stability, and developing cost-effective synthesis methods. COFs also show promise in energy material recovery, biomedical diagnostics, and environmental remediation. Combining COFs with other separation technologies can enhance performance, and integrating AI and robotics in COF design may address current limitations, enabling broader industrial and environmental applications.