Exploring high-efficiency catalysts for the electrochemical hydrogen evolution reaction (HER) in alkaline environments is attractive but remains challenging. Here we report a coordination regulation strategy to tune the atomic structure of Ru cluster catalysts supported on Ti3C2Tx MXene (Ru-Ti3C2Tx) for the HER. We identify that the coordination number (CN) of Ru–Ru could be slightly regulated from 2.1 to 2.8 by adjusting the synthesized temperature so as to achieve an optimal catalytic configuration. The Ru-Ti3C2Tx with a CNRu–Ru of 2.8 exhibits the best catalytic activity with a low overpotential of 96 mV at 10 mA cm–2 and a mass activity about 11.5 times greater than the commercial Pt/C catalyst. Density functional theory calculations demonstrated that the small Ru clusters have a stronger covalent interaction with Ti3C2Tx support leading to an optimal ΔGH* value. This work opens up a general avenue to modulate the coordination environment of catalysts for the HER.