Display omitted •PPy particles make GOM with dye adsorption function for sub-nano dyes removement.•Intercalation of PPy improves the GOM’s stability extremely.•PPy nanoparticles modified GOM resulting in 14 times faster water flux.•PPy inhibits the swelling feature of GOM and exhibits improved separation ability. Graphene oxide-based membrane (GOM) has been massively studied in the dye/water separation field, predominately relying on their 1 nm-sized interlayer distance spacing (D-spacing). However, the inefficient removal of sub-nanosized dye molecules and swelling-induced weak long-term stability are currently two key challenges faced by GOM. In this work, we intercalate the soft polymeric polypyrrole (PPy) nanoparticles into GOM to address such gaps. The strong dye adsorption ability of PPy results in the increase of the sub-nanosized MB molecule rejection rate from 60% for GOM to 97% for GO-PPy membrane (GPM) after the initial filtration treatment. Simultaneously, the nanochannels of GPM are partially expanded, leading to an approximately a ~14 times water permeability (21.14 L m-2h−1 bar−1) improvement over GOM (1.56 L m-2h−1 bar−1). More importantly, the strong hydrogen-bond, electrostatic, and π-π interactions between GO and PPy improve the membrane mechanical stability and further reduce the D-spacing, while the enhanced separation ability of nano-sized dye molecules is also exhibited evidenced by the > 99% rejection rates of CV, EBT, CR, and TB. We consider that our strategy could promote the design and development of the high-performance GOM for nanofiltration applications.