The “ship-in-a-bottle (SIB)” strategy offers a novel pathway for constructing hybrid nanocomposites that possess distinctive structural properties, making them ideal as functional materials. This strategy involves the confinement of guest components within a host material, often leading to precisely controlled particle sizes and unconventional electronic structures that exhibit unique properties. Here, we used a metal–organic framework (CoNi-MOF-74) as the host material to trap ultrafine RuO_x nanoparticles with uniform sizes of approximately 1.3 nm within its microporous structure. The electronic structures of these RuO_x nanoparticles have been thoroughly analyzed through X-ray absorption spectroscopy (XAS) measurement. The synthesized RuO_x@NiCo-MOF-74 demonstrates superior performance for water oxidation, with an overpotential of only 254 mV to reach a current density of 10 mA·cm⁻² in alkaline electrolyte, and shows a mass activity that is enhanced by a factor of 154 (4332 vs. 28.2 A·g_Ru⁻¹) compared to commercial RuO₂ under test conditions at 1.63 V (vs. RHE). This work provides a new perspective on synthesizing organic–inorganic hybrid materials with unique structural properties and superior catalytic performance.