Abstract Two alkali-soluble polysaccharide fractions (ASPs I and II) were extracted from longan fruit pericarp in this work. The results of chemical composition indicated that ASP I and II fractions comprised mainly of polysaccharides, proteins and lignins. Four monosaccharides, namely Xyl, Ara, Glc and Gal, were identified for both ASPs I and II. Xyl was the dominant monosaccharide in the two alkali-soluble polysaccharides with relative molar percentages of >60%. It constructed the backbone in combination with Ara for both ASPs I and II. The analysis of glycosidic linkage indicated that Xyl had two linkages,→3)-Xyl-(1→ and →3, 4)-Xyl-(1→. The substitution at C-4 position indicated that Xyl was of pyranose structure. The infrared spectra of ASPs I and II showed the characteristic bands at approximate 897 cm − 1 which indicated the β-linkage configuration of Xyl. Industrial relevance Hemicellulose has been suggested as an important polysaccharide with good pharmaceutical properties, including immune modulation and anti-cardiovascular diseases. In this work, alkali-soluble polysaccharides were extracted from longan fruit pericarp and fractionated. The structural characteristics were identified by gas chromatography/mass spectrometry and infrared spectrophotometry. The results will be helpful for application of hemicellulose in functional food industry.