The invention discloses an ion exchange system for producing functional oligosaccharide and a using method thereof. The ion exchange system comprises a plurality of groups of cation exchange resin systems and anion exchange resin systems which are distributed in a staggered manner, wherein each group of ion exchange resin system comprises a feeding column, a refining column, a sugar top water column, a leaching column, a regeneration column, a back-washing column and a water top sugar column which sequentially move and circularly operate, and the ion exchange systems are connected in parallel for feeding, connected in series for cleaning, regenerated and subjected to water top sugar. According to the present invention, with the application of the system to refine and treat functional oligosaccharide, the water consumption is saved by 70-75%, the hydrochloric acid unit consumption is saved by 50-70%, the liquid caustic soda unit consumption is saved by 50-70%, the treatment cost of the waste liquid is reduced while the cost is saved, the conductivity and the pH color value of the product are stable, and the system is suitable for wide industrial popularization.