Xylooligosaccharides (XOS) have gained considerable attention worldwide as prebiotics due to their immune-strengthening activity and beneficial gut bacteria development and can be produced from xylan-rich resources by acid hydrolysis. The present study proved the organic acid hydrolysis to be beneficial for XOS yield. In this study, a recyclable and separable organic acid, i.e., furoic acid, was used for hydrolyzing xylan to produce XOS, and the response surface methodology design was applied to maximize the XOS yield; the results indicated that the quadratic model terms of the interaction between reaction temperature and hydrolysis time showed the most significant impact on XOS yields (P < 0.05). The predicted maximum yield of XOS was 49.0% with 1.2% furoic acid at 167°C for 33 min, being close to the experimental value (49.2%), indicating that the fitted models were in good agreement with the experimental results. Meanwhile, the primary byproducts, including xylose and furfural, were concurrently bio-oxidized into xylonic acid and furoic acid by Gluconobacter oxydans and separated by electrodialysis. Subsequently, the furoic acid with low solubility (<3.7%, 25°C) was recovered by natural crystallization. The above results indicate that the use of multi-steps contributes to sustainable XOS production by furoic acid.