The electrochemical nitrogen reduction reaction (eNRR) to NH3 has become an alternative to traditional NH3 production techniques, while developing NRR catalysts with high activity and high selectivity is of great importance. In this study, we systematically investigated the potentiality of dual transition metal (TM) atom anchored electrocatalysts, TM1TM2@C9N4 (TM1, TM2 = 3(4)d TM atoms), for the NRR through the first principles high-throughput screening method. A total of 78 TM1TM2@C9N4 candidates were designed to evaluate their stability, catalytic activity, and selectivity for the NRR. Four TM1TM2@C9N4 candidates (TM1TM2 = NiRu, FeNi, TiNi, and NiZr) with an end-on N2 adsorption configuration, and two candidates (TM1TM2 = TiNi and TiFe) with a side-on adsorption configuration, were screened out with the advantage of suppressing the hydrogen evolution reaction (HER) and exhibiting high NRR activity. Moreover, the catalysts with end-on and side-on N2 adsorption configurations were determined to favor distal and consecutive reaction pathways, respectively, with favorable limiting potentials of only -0.33 V to -0.53 V. Detailed analysis showed that the N2 adsorption and activation are primarily ascribed to the strong back-donation interactions between the d-electrons of TM atoms and the anti-orbitals of an N2 molecule. Our findings pave a way for the rational design and rapid screening of highly active C9N4-based catalysts for the NRR.