Electrochemical nitrate reduction reaction (NO₃RR) to ammonia is a promising approach to address excess N-contamination in aqueous environment but suffers from a limited ammonia yield and selectivity due to the low concentration and sluggish kinetics. This work reports a three-dimensional porous electrode with binary Co₂Cu₁ hydroxy phosphate embedded into the surface of Ni₃Co₁ oxy/hydroxides (CoCu-PH@NiCo/Ni, “PH” means phosphate-hydroxide), which delivers a yield of 4.13 mg·h⁻¹·cm⁻² with a high Faraday efficiency of 92.6% under a low nitrate concentration of 40 mM and provide an impressive stability. This embedded structure of the as-prepared catalyst exhibits unique metal coordination ligands and valence states different from the unitary hydroxy-phosphate. The electrochemical in situ infrared spectra and theoretical calculations revealed that the Co sites with the ability to dissociate water molecular to form adsorbed OH* can effectively provide the required protons for the deoxygenation and hydrogenation steps during NO₃⁻ conversion, thereby, effectively reducing the energy barrier of the key transition states in the NO₃RR process to improve the intrinsic kinetics. We demonstrate that the rational design of binary components with the appropriate ability to activate water molecules as well as the three-dimensional porous skeletal structure are expected to promote effectively the low-concentration nitrates conversion to ammonia.