Carbon-based single-atom catalysts (SACs) have arisen as a revolutionary category of materials in electrocatalytic energy transformation, due to the atomically dispersed metal active sites, tunable coordination microenvironments, and ideal catalytic efficiency. This review systematically examines the rational design strategies and electrochemical applications on nitrogen-doped carbon-based SACs within a rational design, activity elucidation, and application development framework, focusing on critical reactions including hydrogen evolution, oxygen reduction, nitrogen reduction, oxygen evolution, and CO2 reduction. Special emphasis is placed on innovative coordination engineering approaches, such as asymmetrical MNx sites, axial coordination modulation, and bimetallic synergistic sites. These strategies elucidate the mechanisms of symmetry-breaking coordination and multi-ligand coupling in tailoring electronic configurations and intermediate adsorption energetics. Complementary insights from aberration-corrected scanning transmission electron microscopy, synchrotron-based X-ray absorption spectroscopy, and density functional theory calculations are integrated to establish dynamic correlations between atomic-level structural descriptors (coordination number, bond length/angle) and electronic states (d-band center, charge transfer). This synthesis advances quantitative structure–activity relationship models linking coordination environment–electronic properties–catalytic performance. In the future, prospects center on interdisciplinary integration harnessing high-throughput robotic synthesis, artificial intelligence-driven design, and life cycle assessment frameworks to bridge atomic-scale precision with device-level implementation. Such efforts will accelerate the translation of SACs into transformative solutions for fuel cells, green hydrogen production, and carbon–neutral technologies, ultimately reshaping sustainable energy conversion landscapes.