In an in-flow chemical reaction system (A) of the present invention, a sample solution (1) containing glycoprotein is injected into a reaction tube (7) in which an alkaline solution continuously flows. When a mixed solution of the sample solution and the alkaline solution reach a thermostat bath (6), reaction for cleaving a glycoside linkage takes place, thereby separating a carbohydrate chain from glycoprotein. From the solution containing the carbohydrate chain, alkali is removed by using an ion-exchange column (12), so that a fraction of a carbohydrate chain (14) is collected into a sample tube (13). In the in-flow chemical reaction system (A), reaction takes place in minutes, so that reaction time is significantly reduced compared to a conventional method. Thus, a glycoside linkage is readily cleaved with high precision in a short time, thereby separating carbohydrate from a glycoside-linkage-having compound.