Cobalt single atoms on nitrogen-doped carbon (CoSAs/N-C) were successfully synthesized through the pyrolysis of metal-organic supramolecular self-template. Only 0.12 wt% metal-doped CoSAs/N-C anodes bring a rate capacity enhancement of 195 mAh g−1 compared to the blank group of nitrogen-doped carbon electrodes at 0.1 A g−1. In addition, the CoSAs/N-C anodes exhibit remarkable sodium-ion storage capacities of 285 mAh g−1 after 2000 cycles at 1.0 A g−1 and 133 mAh g−1 with an exceptional cycling stability for 10,000 cycles at an ultra-high current density of 20 A g−1, thereby showcasing excellent Na ion storage performance. Ex-situ X-ray photoelectron spectroscopic study demonstrates that some N atoms in CoSAs/N-C can reversibly store and release Na ions during discharge and charge cycles. The full cell assembled with CoSAs/N-C anode and Na3V2(PO4)3 cathode displays Coulombic efficiency of >99.7 % after 200 cycles at 0.5 A g−1. Density functional theory (DFT) calculations further reveal that the presence of single-atom Co results in a decrease in the Na binding energy surrounding pyrrolic-N and pyridinic-N structures. This moderate binding energy may be beneficial for Na ion adsorption and desorption. This study opens up new possibilities of fabricating advanced metal single atom anodes for high-performance sodium-ion batteries.