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Alkali-extracted xylan from lignocellulosics is a promising feedstock for production of prebiotic xylooligosaccharides (XOS). An integrated process was established combining autohydrolysis, nanofiltration and xylanase hydrolysis. Results show that after autohydrolysis 48.37% of xylan was degraded into oligomers and dissolved into the autohydrolysate, of which 57.83% were XOS. By-products and xylose were removed by nanofiltration with discontinuous diafiltration, while high recovery yields of XOS (84.15%) and xylan (87.45%) were obtained. High yields of XOS were obtained by adding xylanase to the autohydrolysates; after enzymatic hydrolysis an XOS yield of 96–98% was obtained. The enzymatic hydrolysates showed positive prebiotic effects on B. adolescentis with an increase in cell concentration by 4.8-fold after fermentation for 24 h. The main products were short-chain fatty acids with carbon balanced during the whole fermentation process. This integrated strategy resulted in a final XOS conversion of 41.22% contrasted to the initial xylan in raw alkali-extracted xylan.