Single-atom catalysts (SACs) have become the forefront and hotspot in energy storage and conversion research, inheriting the advantages of both homogeneous and heterogeneous catalysts. In particular, carbon-supported SACs (CS-SACs) are excellent candidates for many energy storage and conversion applications, due to their maximum atomic efficiency, unique electronic and coordination structures, and beneficial synergistic effects between active catalytic sites and carbon substrates. In this review, we briefly review the atomic-level regulation strategies for optimizing CS-SACs for energy storage and conversion, including coordination structure control, nonmetallic elemental doping, axial coordination design, and polymetallic active site construction. Then we summarize the recent progress of density functional theory studies on designing CS-SACs by the above strategies for electrocatalysis, such as hydrogen evolution reaction, oxygen evolution reaction, oxygen reduction reaction, CO2 reduction reaction, nitrogen reduction reaction, and electrosynthesis of urea, and electrochemical energy storage systems such as monovalent metal-sulfur batteries (Li-S and Na-S batteries). Finally, the current challenges and future opportunities in this emerging field are highlighted. This review will provide a helpful guideline for the rational design of the structure and functionality of CS-SACs, and contribute to material optimizations in applications of energy storage and conversion.