Abstract The alkyne semi‐hydrogenation represents a pivotal process for both purification and value enhancement in the petrochemical and organic synthesis industry. While electrocatalytic hydrogenation using H 2 O as a hydrogen source offers an economical, eco‐friendly, and mild route with potential for integration with renewable energy, state‐of‐the‐art electrocatalysts still suffer from low partial current density (J alkene ) and Faradaic efficiency (FE alkene ) for alkyne semi‐hydrogenation at high bias potentials due to undesired competitive reactions. Herein, a ligand‐mediated surface engineering strategy is developed to tailor the interfacial microenvironment of nanoporous Cu via n‐butyl‐mercaptan modification (NBM‐np‐Cu). The optimized catalyst achieves exceptional alkene selectivity of 98.7%, FE alkene of 82.6% and J alkene of 442 mA cm −2 at −0.7 V vs RHE, substantially outperforming unmodified np‐Cu and previously reported electrocatalysts. This unique combination effectively constructs a hydrophobic interface that promotes optimal coverage of H * intermediates while selectively occupying high‐energy unsaturated sites of np‐Cu and preserving abundant active Cu (111) on nanoporous ligaments. Furthermore, the thiol‐induced electronic modulation facilitates rapid alkene desorption, suppressing over‐hydrogenation. Remarkably, this surface functionalization strategy demonstrates broad applicability across diverse Cu nanostructures, various thiol ligands, and multiple alkyne substrates, underscoring its versatility and potential for scalable electrocatalytic alkyne semi‐hydrogenation under industrially relevant conditions.