Separating viscous emulsions remains a critical challenge since the existing porous sieving membranes suffer from severe pore blocking caused by low liquidity of viscous emulsion. We here develop amphiprotic millimeter-scale collagen nanofibers-based (MCN) membrane for efficient separation of viscous emulsions. The MCN membrane features a free-standing 3D network of self-assembled millimeter-scale collagen nanofibers, which enables capillary effect-induced efficient liquid transport, allowing the separation of viscous emulsion to proceed at a low pressure of 0.3 bar. The MCN membrane enables successful separation of a variety of viscous emulsions (77.3–200.0 mPa•s), which are unable to separate by commercial single-sided poly tetra fluoroethylene (PTFE) and single-sided polyvinylidene fluoride (PVDF) sieving membranes. High separation flux (1582 L m−2 h−1 bar−1) and separation efficiency (99.97%) are simultaneously achieved. The MCN membrane also shows good anti-fouling properties and recycling capability.