For many lignocellulosic substrates, hemicellulose is biphasic upon dilute-acid hydrolysis, which led to a modified percolation process employing simulated two-stage reverse-flow. This process has been proven to attain substantially higher sugar yields and concentrations over the conventional single-stage percolation process. The dilute-acid pretreatment of biomass solubilizes the hemicellulose fraction in the solid biomass, leaving less solid biomass in the reactor and reducing the bed. Therefore, a bed-shrinking mathematic kinetic model was developed to describe the two-stage reverse-flow reactor operated for hydrolyzing biphasic substrates, including hemicellulose, in corn cob/stover mixture (CCSM). The simulation indicates that the shrinking-bed operation increases the sugar yield by about 5%, compared to the nonshrinking bed operation in which 1 reactor volume of Liquid passes through the reactor (i.e., tau = 1.0). A simulated optimal run further reveals that the fast portion of hemicellulose is almost completely hydrolyzed in the first stage, and the slow portion of hemicellulose is hydrolyzed in the second stage. Under optimal conditions, the bed shrank 27% (a near-maximum value), and a sugar yield over 95% was attained.