Sulfoxides are essential intermediates for the production of various chemicals and pharmaceuticals, typically synthesized via direct sulfide oxidation. While current methods generally require harsh conditions and/or hazardous oxidants, electrochemical conversion from sulfide to sulfoxide promises ideal selectivity, sustainability, and energy efficiency while uniquely utilizing water as the green oxygen source. However, achieving efficient electro-organic conversion has been challenging due to sluggish surface oxygenating kinetics under nonaqueous conditions. Here we report the development of a novel amorphous ruthenium oxide catalyst characterized by disorderly connected regular/irregular Ru-O6 octahedra. This unique surface structure significantly boosts the surface water oxidation kinetics in nonaqueous media, enabling a universal electro-oxidation approach for efficient sulfide-to-sulfoxide conversion. Superior performance was achieved under mild conditions (e.g., 99% selectivity, 98% yield, and 95% Faradaic efficiency for methyl phenyl sulfide to methyl phenyl sulfoxide), and this approach applies to a broad scope of sulfide substrates and pharmaceuticals. Scalable productions (12.95 g, 88% FE) under high current densities (>100 mA/cm2) further demonstrate the practical values of this electrocatalytic synthetic methodology. Mechanistic and theoretical investigations elucidate the critical role of disorderly arranged Ru-O octahedral units in enhancing the distributions of bonding orbitals and electronic coupling near the Fermi level, leading to boosted kinetics of surface water oxidation (*OH → *O) and subsequent sulfide oxidation (*O + MPS → *MPSO), which follow an adsorbate evolution mechanism-mediated Eley-Rideal reaction (AEM-ER) pathway. Our results highlight the unique and effective role of atomic disorder in overcoming common kinetic limitations during catalyst optimization, which enables ideal direct selective electro-oxidation of organics in nonaqueous media.