Two-dimensional membranes are considered as the most energy-efficient alternatives to various traditional separation processes. To date, atomically thin hexagonal boron nitride, covalent organic frameworks, graphene, graphene oxide, transition metal carbides and nitrides, layered double hydroxide, transition metal dichalcogenides (TMDCs), and metal-organic frameworks have been extensively investigated for high-performance lamellar membranes, which is due to their tunable physicochemical properties, single-layered structure, and in-plane pore structure. This comprehensive review summarizes the different fabrication methods of TMDC-based membranes and introduces the recent modification strategies to improve their microstructural properties. TMDCs-based membranes for wastewater treatment, desalination, proton exchange, gas separation, and energy devices are extensively discussed. Finally, we highlight the current engineering hurdles and suggest research directions for improving the separation efficiency, stability, and permeability of these membranes.