Concurrent activation of lattice oxygen (O
L) and molecular oxygen (O
2) is crucial for the efficient catalytic oxidation of biomass-derived molecules over metal oxides. Herein, we report that the introduction of ultralow-loading of Ru single atoms (0.42 wt%) into Mn
2O
3 matrix (0.4%Ru–Mn
2O
3) greatly boosts its catalytic activity for the aerobic oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA). The FDCA productivity over the 0.4%Ru–Mn
2O
3 (5.4 mmol
FDCA·g
cat-1·h
-1) is 4.9 times higher than the Mn
2O
3. Especially, this FDCA productivity is also significantly higher than that of existing Ru and Mn-based catalysts. Experimental and theoretical investigations discovered that the Ru single atom facilitated the formation of oxygen vacancy (O
v) in the catalyst, which synergistically weakened the Mn–O bond and promoted the activation of O
L. The co-presence of Ru single atoms and O
v also promote the adsorption and activation of both O
2 and HMF. Consequently, the dehydrogenation reaction energy barrier of the rate-determining step was reduced via both the O
L and chemisorbed O
2 dehydrogenation pathways, thus boosting the catalytic oxidation reactions.