Electrochemical reduction of nitrate to ammonia using electrocatalysts is a promising alternative strategy for both wastewater treatment and production of green ammonia. Numerous tactics have been developed to increase the electrocatalyst’s NO₃RR activity. Herein, we report a unique molecular alignment-dependent NO₃RR performance using α-CuPc and β-CuPc nanostructures as effective electrocatalysts for the ambient synthesis of ammonia. The well-aligned β-CuPc demonstrated an impressive ammonia yield rate of 62 703 μg h⁻¹ mg_cat⁻¹ and a Faradaic efficiency of 96%. In contrast, the less well-aligned α-CuPc exhibited a yield rate of 36 889 μg h⁻¹ mg_cat⁻¹ and a Faradaic efficiency of 61% at −1.1 V vs. RHE under the same conditions. Scanning tunneling microscopy/spectroscopy (STM/S) confirms that the well-aligned β-CuPc exhibits superior transport properties due to optimal interaction of the Cu atom with the nitrogen atom of parallel molecules (dπ–pπ) in its one-dimensional nanostructure, which is clearly reflected in the electrocatalytic performance. Furthermore, theoretical research reveals that the NO₃RR is the predominant process on the β-CuPc catalyst in comparison to the hydrogen evolution reaction, which is verified by gas chromatography, with β-CuPc exhibiting weaker binding of the *NO intermediate at the copper site and a lower overpotential, hence facilitating the NO₃RR relative to α-CuPc.