Electrochemical reduction of CO2 to high-energy chemicals is a promising strategy for achieving carbon-neutral energy circulation. However, designing high-performance electrocatalysts for the CO2 reduction reaction (CO2RR) remains a great challenge. In this work, by means of density functional theory calculations, we systematically investigate the transition metal (TM) anchored on the nitrogen-doped graphene/graphdiyne heterostructure (TM-N4@GRA/GDY) as a single-atom catalyst for CO2 electroreduction applications. The computational results show that Co-N4@GRA/GDY exhibits remarkable activity with a low limiting potential of -0.567 V for the reduction of CO2 to CH4. When the charged Co-N4@GRA/GDY system is immersed in a continuum solvent, the reaction barrier decreases to 0.366 eV, which is ascribed to stronger electron transfer between GDY and transition metal atoms in the GRA/GDY heterostructure. In addition, the GRA/GDY heterostructure system significantly weakens the linear scaling relationship between the adsorption free energy of key CO2 reduction intermediates, which leads to a catalytic activity that is higher than that of the single-GRA system and thus greatly accelerates the CO2RR. The electronic structure analysis reveals that the appropriate d-π interaction will affect the d orbital electron distribution, which is directly relevant to the selectivity and activity of catalysis. We hope these computational results not only provide a potential electrocatalyst candidate but also open up an avenue for improving the catalytic performance for efficient electrochemical CO2RR.