Sc and Y are key rare earth elements and are widely used in lamp phosphors, lasers and high-performance alloys. However, highly efficient extraction and separation of Sc3+ and Y3+ is laborious, harmful, slow, and costly, strongly necessitating more efficient extraction and separation techniques. Here, we produced hydrated Sc3+- and hydrated Y3+-controlled graphene oxide (GO) membranes and find that both hydrated cations were completely self-rejected by the membrane. By combining this self-rejection effect of the larger hydrated Y3+-controlled GO membrane and the rapid passage of the membrane through the smaller hydrated Sc3+, we proposed a strategy to separate Sc3+ and Y3+ by using a hydrated Y3+-controlled GO membrane. The experimental results show that the permeation rate of Sc3+ exceeds that of Y3+ when the separation factor reaches 4.02, which can be attributed to the interlayer sieving effects of the GO membrane. Our finding illustrates the use of a forward osmosis process with a GO membrane for the efficient separation of Sc3+ and Y3+ by interlayer sieving, which provides a new effective and eco-friendly method for the separation of rare earth elements.