The SMB chromatography is used to obtain high purification of fructooligosaccharides (FOS), the mixture of kestose and nystose. SMB operation condition is usually determined by triangle theory or standing wave design when reactions do not occur within columns during experiment. Some of the reactions in columns may considerably affect experimental results. FOS can be hydrolyzed and converted into glucose and fructose during operation. To include the effect of reaction, the concentrations of each component at steady state after hydrolysis were used in simulation. The obtained simulation values are well matched with experimental results except sucrose. For sucrose, the experimental results were different from expected one due to the existence of an intermediate component. FOS is easily hydrolyzed and converted into glucose and fructose in more acidic condition and at higher temperature. Hydrolysis reaction can be prevented by the pretreatment of separation resin with NaOH as well as operation under lower temperature.