To synthesize small and evenly distributed fillers in polymer matrix is important to fulfill the advantage of nanocomposite membranes in overcoming the tradeoff effect between permeability and selectivity. In this study, nanocomposite membranes were prepared by synthesizing calcium oxalate (CaOx) nanoparticles in confined space of the layer-by-layer (LbL) self-assembled polymer network through bio-inspired mineralization. The acfive layer was tightly coated on hydrolyzed polyacrylonitrile substrate with thickness less than 200 nm. The CaOx nanoparticles were uniformly distributed in the polymer matrix with diameter less than 50 nm. The hydrophilicity of the nanocomposite membranes was decreased due to the incorporation of CaOx nanoparticles. And the free volume properties were tuned by creating new polymer/filler interface. At precursor concentration of 1 mM, the permeation flux increased by 14% to 958 g/(m(2)h), the separation factor increased by 2.36 times to 1562 compared to the control membrane, and the membrane showed good operating stability.