In this study, a general strategy is demonstrated to prepare a partially oxidized three-dimensional (3D) porous ruthenium (Ru) aerogel with distinct porous architecture and unique Ru/RuO2 interface. The optimized partially oxidized Ru aerogel catalyst exhibits an exceptional HER performance, which is even superior to the benchmark Pt/C catalyst, and an outstanding OER efficiency that is better than commercial RuO2 in both alkaline and acidic solutions. Furthermore, a two-electrode configuration based on the partially oxidized Ru aerogel as both anode and cathode for the overall water splitting exhibits an ultra-low working voltage of 1.467 V in 1 M KOH and 1.468 V in 0.5 M H2SO4 at 10 mA cm−2 as well as a satisfactory long-term stability, outperforming the device composed of Pt/C||RuO2 catalysts. This research opens up a new avenue to develop highly efficient 3D porous aerogel electrocatalysts toward overall water splitting applications.