Conversion of N2 into NH3 through the electrochemical nitrogen reduction reaction (NRR) under ambient conditions represents a novel green ammonia synthesis method. The main obstacle for NRR is lack of efficient, stable, and cost-effective catalysts. In this work, by using density functional theory calculations, 16 transition metal-modified Co4 clusters supported on graphdiyne (GDY) as potential NRR catalysts were systematically screened. Through the examinations of stability, N2 activation, selectivity, and activity, Ti-, V-, Cr-, Mn-, and Zr-Co3@GDY were identified as the promising candidates toward NRR. Further explorations on the NRR mechanisms and the Pourbaix diagrams suggest that Ti-Co3@GDY was the most promising candidate catalyst, as it has the lowest limiting potential and high stability under the working conditions. The high activities originate from the synergy effect, where the Co3 cluster acts as the electron donor and the heteroatom serves as the single active site throughout the NRR process. Our results offer a new perspective for advancing sustainable NH3 production.