In this present study, novel aqueous-phase catalytic systems, namely spherical Au and Pd nanoparticles (NPs) capped with Cs2 [closo-B12H12], were used to produce ethanol and methanol via direct oxidation of methane in the presence of H2O2 and O2 under mild conditions. The ethanol selectivity surpassed 52.96% and 86.33% at 50 °C, and the productivity reached 8.86 and 25.18 mol·kgcat–1·h–1, respectively. Plausible methane–ethane–ethanol pathway involving free radial •OH radicals was proposed based on the electron paramagnetic resonance (EPR) result. According to the theoretical calculations, the surfaces of {111} plane of Au NPs and {100} plane of Pd NPs were capped with Cs2 [closo-B12H12], and Au–B and Pd–B bonds were consequently formed, respectively. Moreover, the binding energies of Au NPs and Pd NPs capped with Cs2 [closo-B12H12] were calculated to be −128.9 and −230.1 kcal mol−1, respectively. Based on the theoretical calculations, higher binding energy indicates a larger amount of charge on the surfaces of the planes of NPs. A lower peak intensity can lead to the formation of a more stable catalyst with enhanced catalytic activity. Thus, the ethanol selectivity of the as-prepared catalyst was considerably higher than that for methanol.