Corn stover was pretreated with acid under moderate conditions (1.5%, w/w, 121 °C, 60 min), and kinetic enzymolysis experiments were performed on the pretreated substrate using a mixture of Celluclast 1.5 L (20 FPU/g dry substrate) and Novozyme 188 (40 CBU/g dry substrate). Integrated chemical and multi-scale structural methods were then used to characterize both processes. Chemical analysis showed that acid pretreatment removed considerable hemicellulose (from 19.7% in native substrate to 9.28% in acid-pretreated substrate) and achieved a reasonably high conversion efficiency (58.63% of glucose yield) in the subsequent enzymatic hydrolysis. Multi-scale structural analysis indicated that acid pretreatment caused structural changes via cleaving acetyl linkages, solubilizing hemicellulose, relocating cell wall surfaces and enlarging substrate porosity (pore volume increased from 0.0067 cm3/g in native substrate to 0.019 cm3/g in acid-pretreated substrate), thereby improving the polysaccharide digestibility.