The separator with high Young’s modulus can avoid the danger of large-sized dendrites, but regulating the chemical behavior of lithium (Li) at the separator/anode interface can effectively eliminate the dendrite issue. Herein, a polyimine aerogel (PIA) with accurate nitrogen (N) functional design is used as the functional separator in Li metal batteries to promote uniform Li nucleation and suppress the dendrite growth. Specifically, the imine (N1) and protonated tertiary amine (N2) sites in the molecular structure of the PIA are significantly different in electron cloud density (ECD) distribution. The N1 site with higher ECD and the N2 site with lower ECD tend to attract and repulse Li ⁺ through electrostatic interactions, respectively. This synergy effect of the PIA separator accelerates the interfacial Li ⁺ diffusion on the Li anode to sustain a uniform two-dimensional Li nucleation behavior. Meanwhile, the well-defined nanochannels of the PIA separator show high affinity to electrolyte and bring uniform Li ⁺ flux for Li plating/stripping. Consequently, the dendrites are effectively suppressed by the PIA separator in routine carbonate electrolyte, and the Li metal batteries with the PIA separator exhibit high Coulombic efficiency and stable high-rate cycling. These findings demonstrate that the ingenious marriage of special chemical structure designs and hierarchical pores can enable the separator to affect the interfacial Li nucleation behavior.