Microfluidics is of great interest for nano-/micro-fabrication but is conventionally limited inside microchannels. Breaking this restriction and developing 2D-microfluidics is anticipated to expand the potential of microfluidics. Here, by harnessing the capillary effect of porous battery separator, a concept of self-assembling capillary 2D-microfluidics is proposed to achieve well-controlled functional coating onto the separator thin-film. The capillary-assisted liquid tailoring behavior of this 2D-microfluidics is investigated by both experimental and simulation studies, and the capillary number is found as the key parameter controlling the 2D-micofluid thickness. For application studies, zein protein solution is employed for this 2D-microfluidics to generate electrochemical active and self-assembled protein microsphere coating onto the separator after drying. The resultant protein microsphere functionalized separator (PMFS) can physiochemically stabilize the surface of lithium metal anode. First, the PMFS works as spherical template to regulate uniform deposition of lithium ions. Second, similar to sustained drug release, the PMFS releases dissolved protein as functional additive into liquid electrolyte, assisting to form robust solid-electrolyte-interphase with highly conductive Li–C–N component. This work not only proposes a facile self-assembling 2D-microfluidic technology for surface nano-/micro-fabrication, but also brings forth a promising protein-based physicochemical strategy for stabilizing lithium metal anode.