This is to study the effects of various pretreatment methods of agricultural residue, corn stover, and to compare the feature and pros and cons of each method including dilute sulfuric acid(DSA), soaking in aqueous ammonia (SAA), and ammonia recycle percolation (ARP). In order to convert corn stover to ethanol, various pretreatments followed by simultaneous saccharification and co-fermentation (SSCF) were tested and evaluated in terms of ethanol yield. With 3%, w/w of glucan loading using ARP-, DSA-, and SAA-treated solids, SSCFs using recombinant E. coli strain (ATCC® 55124) with commercial enzymes (15 FPU of Spezyme CP/g-glucan and 30 CBU/g-glucan enzyme loading) were tested. In the SSCF tests, 87, 90, and 78% of theoretical maximum ethanol yield were observed using ARP-, DSA-, and SAA-treated solids, respectively, which were 69, 58, and 74% on the basis of total carbohydrates (glucan + xylan) in the untreated corn stover. Ethanol yield of SAA-treated solid was higher than those of ARP- and DSA-treated solids. In addition, SSCF test using treated solids plus pretreated hydrolysate indicated that the DSA-treated hydrolysate showed the strongest inhibition effect on the KO11 strain, whereas the ARP-treated hydrolysate was found to have the second strongest inhibition effect. Bioconversion scheme using SAA pretreatment and SSCF can make the downstream process simple, which is suggested to produce ethanol economically because utilization of hemicellulose in the hydrolysate is not necessary.