A flow-through hydrothermal system was developed to increase the recovery of xylan, the extraction of lignin and the subsequent enzymatic hydrolysis efficiency of rice straw. The impact of the operational parameters of several hydrothermal pretreatment process, such as temperature (170–220 °C), time (10–40min) and flow rate (0–160mL/min), on the subsequent enzymatic hydrolysis and the total sugar yield was studied. In comparison to a batch hydrothermal process, the flow-through hydrothermal process shows improved xylose recovery, lignin removal and total sugar yield. Additionally, the enzymatic hydrolysis efficiency of the pretreated rice straw showed enhanced with xylan removal regardless of changes in the pretreatment's temperature, time and flow rate. Furthermore, the optimal conditions for the flow-through hydrothermal pretreatment were 200 °C for 10min at a flow rate of 160mL/min, which resulted in the almost complete removal of the lignin from rice straw and gave a maximum total sugar yield of 84%.