As the most abundant natural and renewable aromatic compounds, lignin has been recognized as a raw material for producing biofuels and chemicals. The commercial lignin is mostly obtained by pulping processes, such as soda lignin and lignosulfonates, which are operated at harsh conditions and cause high energy consumption and sever water pollution. The commercial lignin has low purity and inhomogeneous structure, which hinder its valorization. Therefore, it is urgent to find a facile, efficient, and environmentally friendly method for lignin fractionation to reduce energy consumption and pollution. As a promising and green solvent, deep eutectic solvent (DES) consists of hydrogen bond donor and hydrogen bond acceptor counterpart in a certain molar ratio that result in the formation of eutectic mixture, showing an unusually low freezing point. DES has the characteristics of simple preparation, high stability, fine biocompatibility, high selectivity and recyclability. In recent years, DES has been widely used in the field of biomass treatment due to the excellent delignification. The fractionation abilities for lignin by different types of DES are quite different. Generally speaking, the fractionation ability for lignin by carboxylic-based DES is stronger than that by amide-based DES. The lignin fractionated by DES has the characteristics of high purity, low molecular mass, and polydispersity, which has an application potential compared with commercial lignin. In this review, it begined with the effect of DES types on the lignin fractionation efficiency followed by the influencing factors (composition of DES, reaction temperature, time, and solid-liquor ratio) on the fractionation efficiency and lignin structure. Additionally, the recycling experiments of DES were introduced. According to the existing challenges in the lignin fractionation with DES, it covers the selection of DES, the combination of other pretreatment methods, optimization of reaction conditions, the recycling of DES, and the valorization of lignin to provide some references for the clean and efficient fractionation of lignin.