Nanofiltration (NF) membranes are commonly supplied in spiral-wound modules, resulting in numerous drawbacks for practical applications (e.g., high operating pressure/pressure drop/costs). Vacuum-driven NF could be a promising and low-cost alternative by utilizing simple components and operating under an ultra-low vacuum pressure (<1 bar). Nevertheless, existing commercial membranes are incapable of achieving practically relevant water flux in such a system. Herein, we fabricated a silk-based membrane with a crumpled and defect-free rejection layer, showing water permeance of 96.2 ± 10 L m-2 h-1 bar-1 and a Na2SO4 rejection of 96.0 ± 0.6% under cross-flow filtration mode. In a vacuum-driven system, the membrane demonstrates a water flux of 56.8 ± 7.1 L m-2 h-1 at a suction pressure of 0.9 bar and high removal rate against various contaminants. Through analysis, silk-based ultra-permeable membranes may offer close to 80% reduction in specific energy consumption and greenhouse gas emissions compared to a commercial benchmark, holding great promise for advancing a more energy-efficient and greener water treatment process and paving the avenue for practical application in real industrial settings.