In biomass pretreatment processes, both the properties of feedstock and process parameters play important roles in the yield of downstream enzymatic hydrolysis. More importantly, like many other industrial processes, the pretreatment system is multivariate and the variables in the system are inter-related to different extents, which means that studying the relationships of the key variables is of critical importance for the improvement of downstream enzymatic saccharification yield. In this work, two multivariate analysis methods of the Principal Component Analysis (PCA) and Partial Least Square (PLS) were employed to characterize the detailed relationships of the key process variables of alkaline sulfite pretreatment of corn stover. The results showed that the total alkali charge is positively correlated with the sugar content in pretreated biomass, lignin removal efficiency, and final sugar yield; pretreatment temperature has negative impact on the recovery of polysaccharides; and total alkali charge is more influential than other pretreatment process variables (such as Na2SO3/NaOH and temperature) under the conditions studied.