In this work, a green and robust pretreatment which integrated acetic acid-catalyzed hydrothermal and wet mechanical pretreatment, was developed to efficiently produce high yield (up to 40.12%) of xylooligosaccharides and digestible substrates from Caffeoyl Shikimate Esterase down-regulated and control poplar wood. Subsequently, superhigh yield (more than 95%) of glucose and residual lignin were obtained after a moderate enzymatic hydrolysis. The residual lignin fraction exhibited a well-preserved β-O-4 linkages (42.06/100Ar) and high S/G ratio (6.42). Subsequently, lignin-derived porous carbon was successfully synthesized, and it exhibited a high specific capacitance of 273.8 F g−1 at 1.0 A g−1 and long cycling stability (remained 98.5% after 10,000 cycles at 5.0 A g−1) compared to control poplar wood, demonstrating that special advantage of this genetically-modified poplar in this integrated process. This work developed an energy-saving and eco-friendly pretreatment technology as a waste-free route for converting different lignocellulosic biomass to multiple products.