In the present work, a theoretical design for the viability of bilayer C4N3 (bi-C4N3) as a promising host material for Li-Se battery was conducted utilizing first-principles calculations. The AA- and AB-stacking configurations of bilayer C4N3 can effectively inhibit the shuttling of high-order polyselenides through the synergistic effect of physical confinement and strong Li-N bonds. Compared to conventional electrolytes, the AA- and AB-stacking bilayer C4N3 demonstrate enhanced adsorption capabilities for the polyselenides. The anchored structures of Se8 or Li2Sen (n = 1, 2, 4, 6, 8) molecules within the bilayer C4N3 exhibit high electrical conductivities, which are beneficial for enhancing the electrochemical performance. The catalytic effects of AA- and AB-stacking bilayer C4N3 were investigated by the reduction of Se8 and the energy barrier associated with the decomposition of Li2Se. The AA- and AB-stacking bilayer C4N3 can significantly decrease the activation barrier and promote the decomposition of Li2Se. The mean square displacement (MSD) curves reveal the pronounceably sluggish Li-ions diffusions in polyselenides within the AA- and AB-stacking bilayer C4N3, which in turn demonstrates the notable prospects in mitigating the shuttle effect.