Single‐atom catalysts (SACs) have emerged as a promising class of catalysts in various fields, owing to their well‐defined active centers, tunable coordination environments, and high reaction selectivity. Among the diverse supports, graphene‐based SACs have garnered significant attention due to their exceptional properties in hydrogenation reactions. This review elucidates recent advancements in theoretical investigations of the electronic and geometric structures of metal SACs, with a focus on modulation strategies such as coordination number adjustment, heteroatom doping, defect site engineering, and frustrated Lewis pair construction. This review emphasizes atomic‐level insights into the hydrogenation reaction mechanism in thermocatalysis, including the activation of the H‐source molecules, hydrogen diffusion, and elementary reaction steps. Strategies for modulating the catalytic activity of SACs are summarized. Lastly, this review offers perspectives on the design of effective graphene‐based SACs from theoretical standpoint, paving the way for future research in this exciting field.