Abstract Fine‐tuning hierarchical transport nanochannels in 2D covalent organic framework nanosheet (CON) membranes for ultrafast and selective molecular separation remains a challenging task in sustainable water purification. Here, a polyelectrolyte‐mediated hierarchical assembly strategy was conceived to precisely control the long‐range stacking order of CONs, which diminishes structural defects and optimizes the size and microenvironment of both intrinsic in‐plane pores and interlayer nanochannels. This dual functionalization of the hierarchical pore channels in CON membrane selectively retards the permeation of organic micropollutants (OMPs) while significantly facilitating the rapid transport of salt ions and water molecules, culminating in unparalleled high water permeance (i.e., 72 L m −2 h −1 bar −1 ) and ions/OMPs selectivity (i.e., 438), outperforming state‐of‐the‐art membranes. This work provides a compelling platform for precise regulation of the pore architecture of CON membranes for ultrafast and selective water decontamination.