Lithium-oxygen batteries with ultrahigh energy density have received considerable attention as of the future energy storage technologies. The development of effective electrocatalysts and a corresponding working mechanism during cycling are critically important for lithium-oxygen batteries. Here, a single cobalt atom electrocatalyst is synthesized for lithium-oxygen batteries by a polymer encapsulation strategy. The isolated moieties of single atom catalysts can effectively regulate the distribution of active sites to form micrometre-sized flower-like lithium peroxide and promote the decomposition of lithium peroxide by a one-electron pathway. The battery with single cobalt atoms can operate with high round-trip efficiency (86.2%) and long-term stability (218 days), which is superior to a commercial 5 wt% platinum/carbon catalyst. We reveal that the synergy between a single atom and the support endows the catalyst with excellent stability and durability. The promising results provide insights into the design of highly efficient catalysts for lithium-oxygen batteries and greatly expand the scope of future investigation.