Electrochemical nitrate reduction reaction (NO3RR) has the dual effect of relieving nitrate contamination and producing the high value-added NH3, which calls for the creation of sophisticated electrodes in order to attain high yield rate, stability, and Faradaic efficiency (FENH3). In this study, iron-based conjugated molecule electrocatalyst, i.e. iron phthalocyanine (FePc), was fabricated into nanorods with excellent crystallinity by a facile precipitation method and applied in NO3RR electrode. The NO3RR performance is enhanced by decorating FePc nanorods on multi-walled carbon nanotubes (CNT) (denoted as FePc@CNT X:10) due to the improved dispersibility and electrical conductivity. The results disclose that FePc@CNT 6:10 exhibits the highest performance with a FENH3 of 94% at −0.45 V (vs. Reversible Hydrogen Electrode) and an ammonia yield rate of 0.35 mmol h−1 mgcat.−1. Notably, a significant NH3 partial current density of approximately 75 mA cm−2 is attained at −0.50 V, correlating with a marginally deteriorated FENH3 of 92.9% and an ammonia yield rate of 0.46 mmol h−1 mgcat.−1. Besides, this catalyst exhibits a long-term NO3RR stability with the ten consecutive cycles. Operando attenuated total reflection surface-enhanced infrared absorptive spectroscopy (ATR-SEIRAS) and density functional theory (DFT) calculations reveal that NO3− undergoes deoxygenation and extensive hydrogenation steps and FePc is more likely to convert NO3− to NH3 under the ONH route. This work provides advanced insights into the rational design of metal phthalocyanine catalysts for electrocatalytic reactions.