Electrochemical CO₂ reduction (ECR) is one of the most effective methods to obtain carbonaceous chemicals and reduce greenhouse gases passingly under the ambient condition. However, efficient electrocatalysts featured with high selectivity and stability are still lacking. A novel molecule-mediated Ag electrocatalyst with capped thiols is rationally designed for high-performance ECR. The thiol-capped and carbon-supported Ag nanostructures (Ag-TC) are formed by in situ electrochemical reduction from three-dimentional (3D) Ag-thiol metal-organic compound with cysteine as the anchor agent and carbon source. Ag-TC exhibits high selectivity and stability for CO₂ conversion to CO (86.7%), which is more catalytically active than that of common Ag nanoparticles. The function of thiols for ECR is proved by replacing cysteine with alanine without thiol group. Meanwhile, alternatively replacing and removing the surface molecules on the Ag foil further demonstrate the effct of thiols. This work enlightens the promise of in situ construction method for molecule capped metal electrocatalyst towards selective and stable ECR.