Abstract Designing excellent electrocatalysts for the hydrogen evolution reaction (HER) is extremely significant in producing clean and sustainable hydrogen fuel. Herein, a rational strategy is developed to fabricate a promising electrocatalyst by introducing atomically dispersed Ru into a cobalt‐based metal‐organic framework (MOF), Co‐BPDC (Co(bpdc)(H 2 O) 2 , BPDC: 4,4'‐Biphenyldicarboxylic acid). The obtained CoRu‐BPDC nanosheet arrays exhibit remarkable HER performance with an overpotential of 37 mV at a current density of 10 mA cm −2 in alkaline media, which is superior to most of the MOF‐based electrocatalysts and comparable to the commercial Pt/C. Synchrotron radiation‐based X‐ray absorption fine structure (XAFS) spectroscopy studies verify that the isolated Ru atoms are dispersed in Co‐BPDC nanosheets with the formation of five‐coordinated Ru‐O 5 species. XAFS spectroscopy combined with density functional theory (DFT) calculations unravels that atomically dispersed Ru can modulate the electronic structure of the as‐obtained Co‐BPDC, contributing to the optimization of binding strength for H* and the enhancement of HER performance. This work opens a new avenue to rationally design highly‐active single‐atom modified MOF‐based HER electrocatalysts via modulating electronic structures of MOF.