Ultrathin β-MnOOH nanofibers can be produced on a large scale via a green-chemical method using an aqueous solution of very dilute Mn(NO3)2 and aminoethanol at room temperature. High-magnification electron microscopy demonstrates that the β-MnOOH nanofibers are 3–5 nm thin and up to 1 micrometer long and the nanofibers are parallel assembled into bundles with an average diameter of 25 nm. By a filtration process, ultrathin mesoporous membranes with strong mechanical, thermal, and chemical stabilities are prepared from the β-MnOOH nanofiber bundles. The membranes can separate 10-nm nanoparticles from water at a flux of 15120 L m−2·h−1·bar−1, which was 2–3 times higher than that of commercial membranes with similar rejection properties. Based on the Young-Laplace equation, β-MnOOH nanofiber/polydimethylsiloxane composite membranes are developed through a novel downstream-side evaporation process. From nanoporous to dense separation membranes can be achieved by optimizing the experimental conditions. The membranes show desirable separation performance for proteins, ethanol/water mixtures, and gases. The synthesis method of β-MnOOH nanofibers is simple and environmentally friendly, and it is easily scalable for industry and applicable to other metal oxide systems. These composite membranes constitute a significant contribution to advanced separation technology.