Single-atom catalysts (SACs) with a TM-N₄-C structure, where a transition metal (TM) atom is embedded in nitrogen-doped graphene, have emerged as promising electrocatalysts for electrochemical nitrogen reduction reaction (eNRR). However, their performance is often limited by weak N₂ adsorption and insufficient activation of the inert N≡N bond. In this work, we propose a novel bilayer catalyst architecture, Mn-N₄-C/MoS₂-TM, by vertically integrating the Mn-N₄-C site with sulfur vacancies (V_s) on the MoS₂ basal plane, where TM dopants are anchored at the V_s sites (denoted as MoS₂-TM). Using first-principles simulations, we investigate the eNRR performance within the interlayer space of this hybrid system. Our results reveal that the confined interlayer region with the dual active site of Mn-N₄-C and MoS₂-TM acts as an efficient nano-reactor, working synergistically to enhance N₂ adsorption and activation. Notably, during catalysis, the active site dynamically shifts between the Mn-N₄-C and MoS₂-TM sites for binding key reaction intermediates, significantly lowering the energy barrier of the potential-determining step, thereby promoting the conversion of N₂ to NH₃. Mechanistic analyses identify Mn-N₄-C/MoS₂-TM (TM = Mn, Tc and Ag) as particularly promising eNRR catalysts, exhibiting a low limiting potential of -0.3 V and a maximum kinetic barrier of 0.75 eV. Furthermore, we develop a novel descriptor, , based solely on intrinsic material properties (i.e., the number of d electrons () and the electronegativity ()) of the TM dopants, which accurately predict eNRR activity across the series. This work presents a unique strategy for rational design of dual site catalysts, opening a new avenue for efficient eNRR electrocatalysts.