The development of cost-effective, robust, and durable electrocatalysts to replace the expensive Pt-based catalysts towards oxygen reduction reaction (ORR) is the trending frontier research topic in renewable energy and electrocatalysis. Particular attention has been paid to metal-nitrogen-carbon (M-N-C) single atom catalysts (SACs) due to their maximized atom utilization efficiency, biomimetic active site, and distinct electronic structure. More importantly, their catalytic properties can be further tailored by rationally regulating the microenvironment of active sites (i.e., M–N coordination number, heteroatom doping and substitution. Herein, we present a comprehensive summary of the recent advancement in the microenvironment regulation of M-N-C SACs towards improved ORR performance. The coordination environment manipulation regarding central metal and coordinated atoms is first discussed, focusing on the structure–function relationship. Apart from the near-range coordination, long-range substrate modulation including heteroatom doping, defect engineering is discussed as well. Besides, the synergy mechanism of nanoparticles and single atom sites to tune the electron cloud density at the active sites is summarized. Finally, we provide the challenges and outlook of the development of M-N-C SACs.