Ultra-thin membrane with nanoscale through hole has great potential in biomedical applications, where precise controllability of porosity, pore size and film thickness is urgently required. The present work proposed a cost-effective way to prepare the ultra-thin nanoporous film with a promising controllability. Monodispersed nanoparticle, rather than photoresist, is used as the sacrificial material for this new lift-off process. By releasing the particles, holes can be achieved with predetermined characters. A 110 nm-thick nanoporous aluminum film with well-controlled pore’s diameter was successfully fabricated to validate the technique. The technique has wider process window and better applicability than other nanofabrication methods.