Anthropogenic nitrate pollution has an adverse impact on the environment and human health. As part of a sustainable nitrate management strategy, electrochemical denitrification is studied as an innovative strategy for nutrients recycling and recovering. It is, however, challenging to selectively electro‐reduce nitrate with low‐concentration for ammonia. Herein, the photo‐deposition of size‐defined Ru nanoclusters (NCs, average size: ≈1.66 nm) on TiO2 nanotubes (NTs) is demonstrated, which show improved performance for nitrate‐to‐ammonia electroreduction with a maximum yield rate of ≈600 µg h−1 cm−2 and a faradic efficiency (FE) of > 90.0% across a broad range of potentials in comparison with electrodeposited Ru nanoparticles (NPs, average size: ≈23.78 nm) on TiO2 NTs. Experimental and theoretical evidence further suggests the small‐size Ru NCs with the intrinsically enhanced selectivity and activity because of the strong metal/substrate interaction and unsaturated coordination state. The findings highlight the size effect on Ru‐based catalyst supported on metal oxides, a versatile catalytic model, which allows the regulation of hydrogen adsorption to favor ammonia production over the competing hydrogen evolution reaction.