Lithium (Li) metal has been regarded as the ideal anode for rechargeable batteries due to its low reduction potential and high theoretical capacity. However, the formation of fatal Li dendrites during repeated cycling shortens the battery life and causes serious safety concerns. Functionalized separators with electrically conductive and lithiophilic coating layers potentially inhibit dendrite formation and growth on Li metal anodes by providing nucleation sites for reversible Li deposition/stripping. In this work, we propose functionalized separators incorporating heteroatom-doped (N or B) graphene interlayers to modulate the Li nucleation behavior. The electronegative N-doping and electropositive B-doping were investigated to understand their regulation of the Li deposition behavior. With the heteroatom-doped graphene-coated separators, we observe significantly improved cycling stability along with enhanced charge transfer kinetics and low Li nucleation overpotential. This is attributed to the heteroatom-doped graphene interlayer expanding the surface area of the Li metal anode while providing additional space for uniform Li deposition/stripping, thus preventing undesirable side reactions. As a result, the formation of dendrites and pits on the Li metal anode surface is suppressed, demonstrating the protective effect of the Li metal anode. Interestingly, N-doped graphene-coated separators exhibit lower Li nucleation overpotentials than B-doped graphene-coated separators but rather lower average Coulombic efficiencies and reduced cycling stability. This implies that adequate adsorption on B-based sites, as opposed to the strong adsorption on N-based sites, improves the reversibility. Notably, the Li adsorption strength of the lithiophilic functional groups critically affects the reversibility, as observed by Li nucleation barrier measurements and atomistic simulations. This work suggests that interface engineering using conductive and lithiophilic materials can be a promising strategy for controlling Li deposition in advanced Li metal batteries.