The graphene oxide (GO) membrane displays promising potential in efficiently filtering ions from water. However, the precise mechanism behind its effectiveness remains elusive, particularly due to the lack of direct experimental evidence at the atomic scale. To shed light on this matter, state‐of‐the‐art techniques are employed such as integrated differential phase contrast‐scanning transmission electron microscopy and electron energy loss spectroscopy, combined with reverse osmosis (RO) filtration experiments using GO membranes. The atomic‐scale observations after the RO experiments directly reveal the binding of various ions including Na+, K+, Ca2+, and Fe3+ to the defects, edges, and functional groups of GO. The remarkable ion‐sieving capabilities of GO membranes are confirmed, which can be attributed to a synergistic interplay of size exclusion, electrostatic interactions, cation–π, and other non‐covalent interactions. Moreover, GO membranes modified by external pressure and cation also demonstrated further enhanced filtration performance for filtration. This study significantly contributes by uncovering the atomic‐scale mechanism responsible for ion sieving in GO membranes. These findings not only enhance the fundamental understanding but also hold substantial potential for the advancement of GO membranes in reverse osmosis (RO) filtration.