The aim of this study is to determine the optimal parameters for the separation of glucose-fructose syrup sugars into glucose, fructose, and oligosaccharides. A mathematical model of chromatographic separation of glucose-fructose syrup (GFS) was constructed. During the optimization of the chromatographic separation process, it was found that the most significant parameter affecting the purity of the fructose yield is the dry matter content. In the course of research, it was found that the dry matter content of 30% is optimal for separating glucose-fructose syrup, at separating the use of this parameter made it possible to obtain a carbohydrate composition with a content of fructose 93%, glucose 5% and oligosaccharides 2%. This is the highest yield of fructose when separated by ion exchange resins of company “Purolite” brand PCR641Ca.