Fenton reaction has been widely used for pretreatment of lignocellulose with the advantages of simple operation, a rapid reaction rate, and less pollution. In this study, batch and fed-batch Fenton reactions to treat corn stover (CS) for carbohydrate utilization were tested. The composition analyses showed that the batch reaction had a greater degree of removal of holocellulose but fed-batch reactions could preserve more hemicellulose. Ultralow enzyme hydrolysis (1 FPU/g) was used to hydrolyze the Fenton reaction-modified CS, and the yield of glucose resulting from batch reaction was 2.5 times higher than that from the raw CS. Surprisingly, a combined catalyst of maleic acid and aluminum chloride (MAAL) was used to catalyze the modified CS for S-hydroxymethylfurfural (HMF) and furfural production, and the highest conversion values for cellulose and hemicellulose achieved were 82 and 95%, respectively. Confirmed by a series of characterizations, this study provides clear insight into the Fenton reaction and how it can alter the lignin structure to facilitate holocellulose utilization.