MXenes are a new type of 2D material, featuring numerous favorable properties, such as excellent flexibility, hydrophilicity, abundant functional groups, and high conductivity. Currently, MXene is a hot topic in the field of membrane separation processes. This timely review presents the recent progress in MXene-based membrane in terms of structural engineering and versatile applications. First, the preparation methods for MXene nanosheets and the fabrication technologies for MXene-based membranes are categorized. Then, the separation-based applications of MXene membranes, including gas separation, water treatment, organic solvent purification, nanofluidic ion transport, and osmotic energy conversion, are summarized. Finally, the bottlenecks that limit the application of MXene-based membranes are outlined, and future research prospects are discussed.