Ruthenium (Ru)-catalyzed aprotic Li–O2 batteries have attracted a great deal of interests because of their excellent electrochemical performances including high specific energy and round-trip efficiency. However, it remains unclear how the incorporated Ru catalysts function to enhance the batteries’ performance. Herein, we report Ru nanocrystal-catalyzed carbon nanotube-based aprotic Li–O2 batteries with electrochemical performances that can match or even surpass some of the best literature results. The catalytic mechanism of Ru nanocrystals has been studied by a combination of Coulometry and in situ differential electrochemical mass spectrometry (DEMS). It has been found that through the synergy of water additive in electrolyte and Ru-based catalysts, the charging reaction overpotential can be brought down to 0.12 V (usually η>1 V). Moreover, an isotope-labeled DEMS study on the electrochemical oxidation of Li213CO3 indicated that Ru nanocrystals also have the capability to decompose Li2CO3, a detrimental by-product formed in almost all aprotic Li–O2 batteries, at a surprisingly low potential of ~3.5 V vs. Li/Li+ (usually >4.0 V). The capabilities of Ru nanocrystals to decompose Li2O2, LiOH, and Li2CO3 at low voltages, which drastically decreases the degradation of electrode and/or electrolyte, are crucial to achieve outstanding electrochemical performances for Li–O2 batteries.