Hydrotropic pretreatment using sodium xylene sulfonate (SXS) could remove lignin and xylan from corn stover to enhance enzymatic saccharification. Peracetic acid (PAA) treatment prior to the hydrotropic process [so-called modified hydrotropic pretreatment (MHP)] could double the delignification efficiency and remarkably increase glucan conversion. After pretreatment, samples were treated by PFI refining for comparison. With the supplement of PFI refining before enzymatic hydrolysis of the MHP-treated corn stover, 87.6% of the glucan yield could be achieved and the corresponding xylan yield was 43.7%. In addition, the pretreated corn stover was analyzed by Fourier transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD), and scanning electron microscopy (SEM). The lignin precipitate from the spend liquor was also investigated by FTIR. The cleavage of the lignin structure could be observed from FTIR results. The crystallinity index (CrI) of corn stover after MHP was increased according to XRD analysis, while the reduction of total CrI of cellulose between pretreatment samples was analyzed by FTIR. SEM analysis demonstrated that PAA treatment affected the morphology of corn stover fiber by generating pores and allowing for better contact of the enzyme to polysaccharides.