Two-dimensional (2D) membranes enable ion-sieving through well-defined subnanoscale channels. In particular, graphene oxide (GO), a representative 2D material with a flexible structure, can be manufactured into various types of membranes, while defects such as pores and wrinkles are readily formed through self-aggregation and self-folding during membrane fabrication. Such defects provide a path for small ionic or molecular species to be easily penetrated between the layers, which deteriorates membrane performance. Here, we demonstrate the effect of shear-induced alignment with continuous agitation on GO membrane structure during pressure-assisted filtration. The shear stress exerted on the GO layers during deposition is controlled by varying the agitation rate and solution viscosity. The well-stacked 2D membrane is obtained via the facile shear-controlled process, leading to an improved salt rejection performance without additional physicochemical modifications. This simple approach can be extensively utilized to prepare the well-ordered structure of other 2D materials in various fields where the defect control is required.