In recent years, people’s continuous attention to energy crisis and environmental problems has promoted the development of electric energy storage technology. The emergence of lithium-ion battery (LIB) has profoundly impacted on society by providing energy storage for portable electronic devices, medical devices and electric vehicles. However, the electrode materials can only contribute a low capacity due to the intercalation reaction chemistry, specific capacity of Li-ion batteries cannot be further improved. Therefore, lithium secondary battery systems with higher energy and power density need to be developed for the next generation of electric vehicles.The lithium metal has an extremely high theoretical specific capacity (3860 mAh/g) and low redox potential (–3.04 V vs. standard hydrogen electrode), giving the lithium battery a high energy density when used as a anode material. And when sulfur used as a cathode material, its theoretical specific capacity reaches 1672 mAh/g, thus the theoretical energy density of the lithium sulfur (Li-S) battery system is as high as 2600 Wh/kg. However, the polysulfides in Li-S battery seriously affect the safety and electrochemical performance of the cell. When lithium metal used as anode materials, the uncontrolled dendrite growth also brings serious safety risks to users. Therefore, all the basic components of lithium batteries, including the anode, cathode, separator and electrolyte, need to be optimized. Most of the current research has focused on the development of high-capacity anode and cathode materials. In fact, functional separators have an important impact on the safety and electrochemical performance of lithium secondary batteries. Compared with other materials that modified commercial polyolefin membranes, two-dimensional materials offer the advantages of ultra-thin laminate structure, high mechanical strength, high specific area, and adjustable surface chemical properties. Therefore, in Li-S batteries, two-dimensional material-functionalized separators can inhibit the shuttle effect of polysulfides through chemical adsorption and confined pore channels. In Li-metal batteries, the inhibition of dendritic growth by two-dimensional functional membranes is mainly due to its high mechanical strength, thermal conductivity and the ability to regulate ion transport flux through defect sites. And in Li-ion batteries, the two-dimensional functional separator mainly improves the wettability and poor thermal stability of routine polyolefin membrane, thus it greatly enhances the electrochemical performance and safety performance of lithium cells. This review first introduces the unique advantages of two-dimensional materials in the membrane, including parallel self-assembly feature, excellent mechanical strength and flexibility, ultrahigh specific surface area, surfaces are easily modified and element doped and ultrathin laminar structure. Then the review briefly describes the method of constructing two-dimensional materials separators and its characterization. Subsequently, this paper focuses on the application of different types of two-dimensional materials functional membranes in solving polysulfide shuttle effect in Li-S batteries, dendrite growth of anode in Li-metal batteries, as well as poor wettability and thermal stability of commercial separator in Li-ion batteries. Finally, the remaining opportunities and challenges of two-dimensional materials in Li battery separator materials are briefly discussed.