Encapsulating metal‐based catalysts inside carbon sheaths is a frequently‐adopted strategy to enhance their durability under various harsh situations and improve their catalytic activity simultaneously. Such carbon encapsulation, however, imposes significant complications for directly modifying materials’ surface atomic/electronic configurations, fundamentally impeding the accurate tuning of their catalytic capabilities. Herein, a universal single‐atom alloy (SAA) strategy is reported to indirectly yet precisely manipulate the surface electronic structure of carbon‐encapsulated electrocatalysts. By versatilely constructing a SAA core inside an N‐doped carbon sheath, material's electrocatalytic capability can be flexibly tuned. The one with Ru‐SAA cores serves as an excellent bifunctional electrocatalyst for oxygen/hydrogen evolution, exhibiting minimal cell voltage of 1.55 V (10 mA cm−2) and outstanding mass activity of 1251 mA mgRu−1${\rm{g}}_{{\rm{Ru}}}^{ - 1}$ for overall water splitting, while the one with Ir‐SAA cores possesses superior oxygen reduction activity with a half‐wave potential of 919 mV. Density functional theory calculations reveal that the doped atoms can simultaneously optimize the adsorption of protons (H*) and oxygenated intermediates (OH*, O*, and OOH*) to achieve the remarkable thermoneutral hydrogen evolution and enhanced oxygen evolution. This work thus demonstrates a versatile strategy to precisely modify the surface electronic properties of carbon‐shielded materials for optimized performances. A universal single‐atom alloy strategy is proposed to precisely manipulate the surface electronic structure of carbon‐encapsulated electrocatalysts, thus simultaneously achieving the catalytic multifunctionality, catalytic activity promotion, and durability maintenance. Theoretical calculation discloses the relationship among various single atoms, surface electronic structures, and the resulted electrocatalytic hydrogen/oxygen evolution behavior. This study demonstrates a versatile strategy to precisely modify the surface electronic properties of carbon‐shielded materials for optimized performances.