The cost-effective and low-carbon fractionation of lignocellulosic biomass will enhance the economic viability of bio-refining. To achieve efficient reed fractionation under favorable conditions, microwave-assisted choline chloride and p-toluene sulfonic acid (M-ChCl/p-TsOH) pretreatment was employed. The fractionation of reed components demonstrated higher effectiveness with M-ChCl/p-TsOH pretreatment compared to conventional DES pretreatment. Under M-ChCl/p-TsOH conditions, a high hemicellulose removal rate (∼90%) and delignification rate (∼65%) were achieved while achieving a saccharification rate of 88% during cellulase hydrolysis. Microwave assistance not only significantly reduced reaction time to less than 60 s but also enhanced the pretreatment efficacy. Furthermore, the obtained lignin products consisted of low-polymerization lignin (MW < 800 g/mol) and acid-soluble lignin, providing a solid foundation for subsequent high-value utilization of lignin. This study provides a promising strategy for the low carbon fractionation of reed using DES, aiming to simultaneously achieve efficient cellulose hydrolysis and obtain tractable lignin.