As a new sweetener, fructooligosaccharide is paid more and more attention for its health improvement property. It includes trisaccharide, tetrasaccharide and pentasaccharide, and can be produced from sucrose by the fermentation of microorganism. In order to analyze the content of fructooligosaccharide in fermented sugar by gas chromatography, fructooligosaccharide was transformed into trimethylsilyl derivatives. Based on the modified gas chromatograph SP2308, and under the chosen chromatographic conditions with 0.53 mm capillary column of OV-101, the contents of fructose, glucose, sucrose and fructooligosaccharide were determined by programmed temperature chromatography. The recovery of fructooligosaccharide was satisfactory.