The interlayer spacing (i.e., d-spacing) plays a crucial role in determining the selectivity and permeability of nanofiltration membranes. A high-throughput directional filtration can be achieved by designing and controlling the d-spacing. In this study, the d-spacing of a graphene oxide (GO) membrane was tuned and fixed to the desired value (approximately 0.79 nm) using a solution of polyethyleneimine (PEI) and GO at a PEI/GO mass ratio of 15:1. The resultant PEI/GO was deposited on a polyacrylonitrile (PAN) substrate to form a robust composite nanofiltration membrane (a PEI/GO@PAN membrane). The as-prepared membrane exhibited an ultrahigh flux of 117.8 L·m−2·h−1, and the rejection values for Direct Red 80 (DR80) and Na2SO4 reached 99.7% and < 1.7%, respectively; these are desirable values for dye/salt separation. The PEI/GO@PAN membrane exhibited an excellent filtration performance, and had a longer lifespan and excellent reusability because of its reinforced nature. This work suggested that tuning the d-spacing with PEI would be an effective strategy to achieve the anticipated functions of nanofiltration membranes.