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Laminar structure membranes assembled with two-dimensional materials, such as graphene oxide (GO), have attracted wide attention from researchers in waste water treatment. However, it is still a challenge to obtain high-performance membranes by precisely controlling the channel of water permeation. In this work, a series of GO nanosheets and silica (SiO2) nanoparticles were employed to adjust the channel microstructure of GO/SiO2 composite nanofiltration membranes. In general, the use of small-size GO nanosheets in the composite membrane could short the length of the transverse channels between the GO nanosheets and increase the amount of the longitudinal pores among the GO nanosheet edges, thus largely enhancing the water flux of the composite membrane. The addition of small-size SiO2 nanoparticles in the composite membrane could help to form a continuous transverse channel of water permeation, and also greatly raise the water flux. The results showed that the composite membrane prepared with GO (1.2 μm) and SiO2 nanoparticle (25 nm, 30 wt% of the GO mass), had the best performance, the pure water flux was 72.8 L m−2 h−1, and the rejection rate for the dyes was>99.4 %. After being recycled for 8 times, the rejection rate for the dyes was still as high as 97.5%. This work showed that controlling the size of nanosheets and nanoparticles could effectively adjust the channel microstructure of the composite membranes, which was very important for the membrane performance.