To obtain the total fractionation and pretreatment of the corn stover, two-stage percolation process was investigated. This process consists of two steps: use of 0.07 wt% sulfuric acid for hemicellulose recovery in first stage and ARP (ammonia recycled percolation) in the following stage for lignin recovery. Among tested conditions, the best conditions of two-stage process were as follows: 1st stage; 170 ℃, 2.5 ml/min, 30 minutes using 0.07 wt% sulfuric acid and 2nd stage; 170 ℃, 5.0 ml/min, 60minutes using 15 wt% ammonium hydroxide. At above two-stage treatment conditions, the hemicellulose in corn stover was easily hydrolyzed (95%) and recovered with high yields (86%) and the extent of the lignin removal was 81%. After two-stage process, the treated biomass contained nearly pure glucan (85%). Two-stage treatment brought about enzymatic digestibility of 90% and 89% with 60 and 15 FPU/g glucan cellulase enzyme loadings, respectively.