Producing hydrogen from the abundant seawater is very attractive for the sustainable development of hydrogen energy. Rational design and construction of efficient bifunctional catalysts remain a huge challenge. Herein, we report a novel N-doped carbon polyhedral (NCP) encapsulated Co₃O₄-RuO₂ heterostructure (Co₃O₄-RuO₂@NCP) synthesized through a simple “template-assistance-self-assembly-pyrolysis” strategy for both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) in seawater. The Co₃O₄-RuO₂@NCP catalyst only needs 18 and 250 mV in 1 M KOH, 24 and 260 mV in simulated seawater, 29 and 290 mV in natural seawater to arrive the current density of 10 mA·cm⁻² for HER and OER, respectively. Meanwhile, only 1.53 and 1.60 V are required to drive 10 mA·cm⁻² for overall water splitting in 1 M KOH and natural seawater splitting with good stability and high Faraday efficiency. The combined spectroscopy analysis suggested Ru plays a crucial role in this electrolysis process. During the alkaline HER process, Ru⁴⁺ is partially reduced to Ru(0), and the in-situ formed Ru-Co₃O₄ serves as the active center to promote H₂ evolution. While in the alkaline OER process, partial oxidation of Ru occurs, which enhances the electronic coupling with oxygen-containing species and facilitates the OER process. Density functional theory (DFT) calculations also suggested these structural properties optimized the adsorption and activation process of key active species in the electrolysis process, and the electronic interaction between NC and Co₃O₄-RuO₂ enhanced the activity and selectivity in seawater electrolysis under alkaline conditions. This work developed a promising bifunctional electrocatalyst for natural seawater splitting.