Genetic engineering is considered a promising approach to decrease “biomass recalcitrance” and enhance the lignin valorization. Caffeoyl Shikimate Esterase (CSE) was recently indicated to play an important role in lignin biosynthesis. However, the effect of this enzyme on poplar lignin structure and subsequent treatment has not been systematically analyzed. In this study, ultrafast microwave-assisted deep eutectic solvents (DES) pretreatment was effectively performed to deconstruct the main components in wild-type (WT) and CSE down-regulated poplar. After pretreatment with two kinds of DES (ethylene glycol-based and glycerol-based DES), the saccharification efficiency of CSE down-regulated poplar was significantly improved, reaching 96.15%. In addition, the yield of DES lignin increased to 62.66% and 72.89% after Ethylene Glycol and Glycerol-based DES pretreatment in CSE poplar woods as compared to WT poplar wood (48.06% and 60.47%). Moreover, structural and morphological variations of lignin after CSE down-regulation and DES pretreatments have been systematically studied by 2D-HSQC, 31P NMR, GPC, SEM, and TEM techniques. Results showed that native lignin from WT and CSE down-regulated poplars had similar structural features excepted for high content of H-type and p-hydroxybenzoate (PB) units in the CSE down-regulated poplar lignin. Furthermore, quantification of different linkages (β-O-4, β-β, β-5, etc.) in native lignin and DES lignin fractions suggested the ultrafast DES fractionation resulted in the significant cleavage of these linkages under glycerol-based DES pretreatment. Meanwhile, the DES lignin from glycerol-based DES pretreatment was found to be small and homogeneous lignin nanoparticles (LNPs). In short, the glycerol-based DES pretreatment is an environmentally benign scheme to produce easily digestible biomass and the LNPs with narrow size distribution. These findings are very important in assessing the fabricability of CSE poplar in the current biorefinery scenario.