Heterogeneous molecular catalysts, such as metal phthalocyanines, are efficient electrocatalysts for CO2 reduction reaction (CO2RR). However, the rational design and synthesis of a molecular catalyst-based heterostructure for CO2RR remains challenging. Herein, we developed a crystalline bimetallic phthalocyanine heterostructure electrocatalyst (CoPc/FePc HS), which achieved an excellent CO2-to-CO conversion efficiency (99%) and outstanding long-term stability after 10 h of electrocatalysis. Density functional theory calculations revealed that the enhancement of CO2RR performance could be attributed to the distinct electron transfer pattern between FePc and CoPc. The heterostructural engineering in molecular catalysts would inspire a unique approach for improving CO2RR performance.