Recently, metal-based atomically thin materials (M-ATMs) have experienced rapid development due to their large specific surface areas, abundant electrochemically accessible sites, attractive surface chemistry, and strong in-plane chemical bonds. These characteristics make them highly desirable for energy-related conversion reactions. However, the insufficient active sites and slow reaction kinetics leading to unsatisfactory electrocatalytic performance limited their commercial application. To address these issues, defect engineering of M-ATMs has emerged to increase the active sites, modify the electronic structure, and enhance the catalytic reactivity and stability. This review provides a comprehensive summary of defect engineering strategies for M-ATM nanostructures, including vacancy creation, heteroatom doping, amorphous phase/grain boundary generation, and heterointerface construction. Introducing recent advancements in the application of M-ATMs in electrochemical small molecule conversion reactions (e.g., hydrogen, oxygen, carbon dioxide, nitrogen, and sulfur), which can contribute to a circular economy by recycling molecules like H