Electrocatalytic C-N coupling from carbon dioxide and nitrate provides a sustainable alternative to the conventional energy-intensive urea synthetic protocol, enabling wastes upgrading and value-added products synthesis. The design of efficient and stable electrocatalysts is vital to promote the development of electrocatalytic urea synthesis. In this work, copper phthalocyanine (CuPc) is adopted as a modeling catalyst toward urea synthesis owing to its accurate and adjustable active configurations. Combining experimental and theoretical studies, it can be observed that the intramolecular Cu-N coordination can be strengthened with optimization in electronic structure by amino substitution (CuPc-Amino) and the electrochemically induced demetallation is efficiently suppressed, serving as the origination of its excellent activity and stability. Compared to that of CuPc (the maximum urea yield rate of 39.9 ± 1.9 mmol h⁻¹g⁻¹ with 67.4% of decay in 10 test cycles), a high rate of 103.1 ± 5.3 mmol h⁻¹g⁻¹ and remarkable catalytic durability have been achieved on CuPc-Amino. Isotope-labelling operando electrochemical spectroscopy measurements are performed to disclose reaction mechanisms and validate the C-N coupling processes. This work proposes a unique scheme for the rational design of molecular electrocatalysts for urea synthesis.