Transition metal carbides/nitrides/carbonitrides, commonly referred to as MXenes, have gained widespread attention since their discovery in 2011 as a promising family of two-dimensional (2D) materials. Their impressive chemical, electrical, thermal, mechanical, and biological properties have fueled a surge in research focused on the synthesis and application of MXenes in various fields, including membrane-based separation. By engineering the materials and membrane structures, MXene-based membranes have demonstrated remarkable separation performance and added functionalities, such as antifouling and photocatalytic properties. In this review, we aim to have a timely and critical review of research on their fabrication strategy and performance in advanced molecular separation and ion exchange, beginning with a brief introduction of the preparation and physicochemical properties of MXenes. Finally, outlooks and future works are outlined with the aims to provide valuable insights and guidance for advancing membranes’ applications in different separation domains.