Hydrogen-bonded organic frameworks (HOFs) are a new class of crystalline porous materials that are formed through the interconnection of organic or metal–organic building units via intermolecular hydrogen bonds. The remarkable flexibility and reversibility of hydrogen bonds, coupled with the customizable nature of organic units, endow HOFs with mild synthesis conditions, high crystallinity, solvent processability, and facile self-healing and regeneration properties. Consequently, these features have garnered significant attention across various fields, particularly in the realm of membrane separation. Herein, we present an overview of the recent advances in HOF-based membranes, including their advanced fabrication strategies and fascinating applications in membrane separation. To attain the desired HOF-based membranes, careful consideration is dedicated to crucial factors such as pore size, stability, hydrophilicity/hydrophobicity, and surface charge of the HOFs. Additionally, diverse preparation methods for HOF-based membranes, including blending, in situ growth, solution-processing, and electrophoretic deposition, have been analyzed. Furthermore, applications of HOF-based membranes in gas separation, water treatment, fuel cells, and other emerging application areas are presented. Finally, the challenges and prospects of HOF-based membranes are critically pointed out.