The electrochemical NO reduction reaction (NORR) to NH3 offers an efficient, environmentally friendly strategy for NO removal and NH3 production, but developing effective catalysts to facilitate the conversion of NO into NH3 remains a challenge. Single-cluster catalysts (SCCs) with multi-metallic sites show promise due to the synergistic interactions among the active atoms. Herein, utilizing density functional theory (DFT) and grand-canonical DFT (GC-DFT), we systematically investigated the potential of late transition metal (TM = Fe, Co, Ni, Cu, Ru, Rh, Pd, Pt) clusters on graphdiyne (TMx/GDY, x = 1–5) for NORR. Ni3/GDY, Pd3/GDY, and Pt3/GDY emerged as the most promising candidates, demonstrating stability, excellent NORR activity, and HER suppression. Their outstanding performance is attributed to the moderate adsorption of NO, with the dxz/dyz orbitals playing a key role in NO activation. GC-DFT results highlight nonlinear variation of intermediate grand free energies with the applied potential. Detailed electronic property analyses were conducted to reveal the charge effects induced by the applied chemical potential. This study provides valuable insights into SCC-catalyzed NO reduction and highlights the significance of potential effects in theoretical simulations of electrochemical systems.